Finalize app

README.md

@@ -1,42 +1,70 @@
+---
+title: AutoKG
+app_file: main.py
+sdk: gradio
+sdk_version: 3.39.0
+---
 # AutoKG
 
 Using large language models (ChatGPT) to automatically construct a knowledge graph from unstructured plain text.
 
 ## Usage
 
+### Local Gradio app
+
+To locally launch the `Gradio` app from the command line, use
+
+```
+python main.py
 ```
-python text2kg.py <infile> [-h] [--output OUTPUT] [--cookbook COOKBOOK] [--recipe RECIPE] [--thoughts]
+
+### Within a `python` IDE
+
+Import the primary pipeline method using
+
+```python
+>>> from main import create_knowledge_graph
 ```
 
-**Parameters**
+**`create_knowledge_graph` parameters**
 
 ```
-infile
-    path to input text file (assumed to be in plain text form)
---output
-    directory to save results to (default: ./output)
---cookbook
-    path to JSON file containing GPT prompts (default: ./recipes.json)
---recipe
-    recipe to execute, must be a valid name from cookbook (see above)
---thoughts
-    optional flag to save intermediary GPT prompts/replies
+api_key (str)
+    OpenAI API key
+ngram_size (int)
+    Number of sentences per forward pass
+axiomatize (bool)
+    Whether to decompose sentences into simpler axioms as a
+    pre-processing step. Doubles the amount of calls to ChatGPT
+text (str)
+    Input text to extract knowledge graph from
+progress
+    Progress bar. The default is Gradio's progress bar; 
+    set `progress = tqdm` for implementations outside of Gradio
 ```
 
-In my experiments, the rate of the processing is about 2 seconds per sentence per pipeline step.
+### Using Gradio API
+
+Read more [here](https://www.gradio.app/docs/python-client).
 
 ## File structure
 
-### [`data`](./data/)
+```
+chains.py
+    Converts schema.yml items to LangChain chains
+
+environment.yml
+    Contains packages required to run environment
+
+main.py
+    Main pipeline/app code
 
-Name | Description | Source
---- | --- | ---
-`data/openstax/...` | Sections from various OpenStax textbooks. | 
-`data/Seq2KG/...` | Processed test datasets from Seq2KG paper. ("Processing" = merging tokens back to sentences) | [GitHub](https://github.com/Michael-Stewart-Webdev/Seq2KG/tree/master)
+README.md
+    This file
 
-## References
+schema.yml
+    Contains definitions of prompts
 
-1. A case study in bootstrapping ontology graphs from textbooks. (V. K. Chaudhri et al., 2021)
-2. Seq2KG: an end-to-end neural model for domain agnostic knowledge graph (not text graph) construction from text. (M. Stewart & W. Liu, 2020)
-3. Language models are open knowledge graphs. (C. Wang et al., 2020)
-4. ProofWriter: generating implications, proofs, and abductive statements over natural language. (O. Tafjord et al., 2020)
+utils.py
+    Contains helper functions
+```

data/Seq2KG/bbn.txt

@@ -1,166 +0,0 @@
-"It's just like weather forecasting," says Energy Transportation trial attorney Harry Reasoner of Vinson & Elkins.
-Forecasting is only one part of Litigation Sciences' work.
-Instead, Mr. Vinson says, interviews with thousands of jurors reveal that they start with firmly entrenched attitudes and try to shoe-horn the facts of the case to fit their views.
-Someone with a master's degree in classical arts who works in a deli would be ideal, Litigation Sciences advises.
-(Since Litigation Sciences generally represents the defense, its job is usually to help the lawyers identify and remove such people from the jury.)
-He heads Litigation Sciences Inc., the nation's largest legal consulting firm, which is helping corporate America prepare for high-stakes litigation by predicting and shaping jurors'reactions.
-In the process, Litigation Sciences is quietly but inexorably reshaping the world of law.
-Little known outside the legal world but a powerhouse within, Litigation Sciences, a unit of Saatchi & Saatchi PLC, employs more than 100 psychologists, sociologists, marketers, graphic artists and technicians.
-Recently, Litigation Sciences helped Pennzoil Co. win a $10.5 billion jury verdict against Texaco Inc.
-It advised the National Football League in its largely successful defense of antitrust charges by the United States Football League.
-A recall of the mushrooms blamed for the food poisoning began in early March.
-In 1987, China exported 65 million pounds of mushrooms, valued at $47 million, to the U.S..
-A spokesman for the Chinese Embassy here said that the Beijing government has taken "many effective measures" to stop the mushroom contamination and is further investigating the underlying causes.
-The management turnover at Reebok International Ltd. continued with the resignation of company president C. Joseph LaBonte, who joined Reebok just two years ago.
-Mr. LaBonte's departure follows by two months the resignation of Mark Goldston as senior vice president and chief marketing officer after only 11 months at Reebok.
-Unreported alimony income can be spotted by computer because a payer of alimony (who gets a deduction) must report the former spouse's Social Security number.
-Passport applicants now must give Social Security numbers, enabling the IRS to see whether Americans living abroad are filing required U.S. returns.
-But while IRS computers focus routinely on target groups like these, the agency has assigned many agents to special projects that need more personal attention.
-In most cases, the IRS says, these projects are local or regional, rather than national, and arise because auditors in an area detect some pattern of abuse among, say, factory workers claiming that having a multitude of dependents frees them from tax withholding or yacht owners deducting losses from sideline charter businesses.
-The national office currently has 21 noncriminal audit projects, according to Marshall V. Washburn, deputy assistant commissioner for examination.
-Mr. Lipstein's absence from the meeting here raised speculation that the sale is in trouble.
-Mr. Lipstein said in a telephone interview from New York that the sale was proceeding as planned.
-"Magazines can no longer be considered institutions," said James Autry, president of Meredith Corp.'s magazine group.
-More than ever, independent magazines and small publishing groups are being gobbled up by larger publishing groups, such as American Express Publishing Corp., a unit of American Express Co., and Conde Nast Publications Inc., a unit of Advance Publications Inc., which are consolidating in order to gain leverage with advertisers.
-Unknown to Mr. Tharp, he had fouled his net on a special IRS project to catch catfish farmers and haulers inclined to cheat on their taxes.
-Confronted with the evidence, Mr. Tharp pleaded guilty to one charge of filing a false return and was fined $5,000 and sentenced to 18 months in prison.
-Many professions long have seemed to be targets because of the exotic or ludicrous efforts of some members to offset high income with fake losses from phony tax shelters: dentists who invested in dubiously dubbed foreign films or airline pilots who raised racehorses on their days off.
-The IRS recently won part of its long-running battle with the Church of Scientology over exemptions when the U.S. Supreme Court held that members' payments to the church weren't deductible because the members received services in return.
-IRS statistics show that the more persistent hiders of income among sole proprietors of businesses include used-car dealers, entertainment producers, masons, roofers, and taxi owners.
-For example, Toronto-based Telemedia Inc. will publish Eating Well, a new food and health magazine due out next summer.
-New York-based Hearst Corp. this fall plans to publish its first issue of 9 Months, a magazine for expectant mothers, and has already launched American Home.
-And Time Warner Inc. is developing a spinoff of Time magazine aimed at kids, on the heels of its successful Sports Illustrated for Kids.
-Over the past four years, the number of consumer magazines has increased by an average of 80 magazines annually, according to Donald Kummerfeld, president of the Magazine Publishers of America.
-Mr. Schwartz is a business executive and writer in New York.
-"I would say he's definitely not in need of money," says Matt Merola, an agent of Mr. Jackson's based in New York.
-Reggie Jackson, the retired baseball star, has found another use for them.
-Mr. Jackson, who won the nickname "Mr. October" for his World Series exploits, is selling some of his canceled checks to autograph collectors through a dealer for as much as $500 each.
-"I don't know of any living ballplayer that's ever done it," says Jack Smalling, a dealer in Ames, Iowa, and a recognized expert in the field of baseball autographs.
-Ramada, which first delayed and then shelved a $400 million junk bond sale that was designed to help finance a restructuring, fell 15.6% to close at 9.
-Ramada has said it hopes to propose a new restructuring plan but hasn't indicated when it will do so.
-Shares of American Medical International, which agreed last week to accept a lower price from a buy-out group that includes First Boston Corp. and the Pritzker family of Chicago, fell 15.8% on Friday to close at 20.
-The buy-out group is offering $26.50 a share for 63 million American Medical shares, down from its offer in July of $28 a share for 68.8 million shares.
-Hilton Hotels, for example, was among the worst-hit issues, falling 20.2% to close at 85, down 21 on Friday.
-McCaw is offering $125 a share for 22 million LIN shares, thereby challenging LIN's proposal to spin off its television properties, pay shareholders a $20-a-share special dividend and combine its cellular-telephone operations with BellSouth's cellular business.
-On Friday, LIN shares were among the few takeover issues that didn't fall much, dropping 5, or 4.9%, to close at 107.
-Traders and investment bankers said LIN shares weren't hurt much because BellSouth is viewed as a well-financed corporate buyer unlikely to be affected by skittishness among bankers or bond buyers.
-Potential bidders for companies "were saying that things were beginning to look expensive," says Mr. Rattner of Lazard.
-Freeport-McMoRan said the shutdown won't affect sales volumes under long-term sales contracts of its Freeport Uranium Recovery Co. unit, but will reduce the amount of product sold on the spot market.
-Freeport-McMoRan Resource Partners, as owner of the uranium-recovery technology, receives royalty payments.
-"The market is overvalued, not cheap," says Alan Gaines of the New York money-management firm Gaines Berland.
-"You had a week of a deteriorating junk-bond market that ran smack into the news on Friday about what appeared to be happening to the bank debt market," says Steven Rattner, a partner and merger specialist with Lazard Freres & Co.
-It was the latest in a series of setbacks for the junk bond market, where prices began weakening last month after Campeau hit a cash crunch.
-Diane S. Killory will join 500-lawyer Morrison & Foerster as a partner in its Washington, D.C., office in mid-November.
-She will help develop the mass-media practice of the San Francisco-based firm's communications group.
-Ms. Killory, 35 years old, resigned as Federal Communications Commission general counsel early this month after nearly three years in that post.
-She was the first woman to be appointed FCC general counsel.
-RICHARD P. MAGURNO, formerly Eastern Airlines'top lawyer, joined the New York law firm of Lord Day & Lord, Barrett Smith as a partner.
-The EC and Japan -- the U.S.'s largest steel suppliers -- haven't been filling their quotas to the full extent.
-The EC steel industry, which has been coping with strong European demand, has been supplying about 5% of the U.S. market compared with recent quotas of about 6.7%.
-Japan has been shipping steel to total about 4.5% of the U.S. market compared with a quota of 5.9%.
-In the recent talks, the EC had its quota increased about 300,000 tons, to 7% of the U.S. market from 6.7% in 1988.
-Japan, however, has agreed to cut its quota to about 5% from 5.9% previously.
-The state has combed through records relating to architects, stockbrokers, lawyers in the New York City area, construction workers from out of the state, and homeowners who claim to be residents of other states -- especially Florida, which has no personal income tax.
-Soon to feel the glare of attention are lawyers elsewhere in the state, doctors, dentists, and accountants, says Frederick G. Hicks, director of the tax-department division that develops the computer-matching programs.
-Mr. Schmedel is editor of The Wall Street Journal's Tax Report column.
-But the product, which wasn't as concentrated as the new Cheer, bombed in a market test in Denver and was dropped.
-P&G and others also have tried repeatedly to hook consumers on detergent and fabric softener combinations in pouches, but they haven't sold well, despite the convenience.
-But P&G contends the new Cheer is a unique formula that also offers an ingredient that prevents colors from fading.
-"When shelf space was cheap, bigger was better," says Hugh Zurkuhlen, an analyst at Salomon Bros.
-Greece's bilateral relations with the U.S. need attention soon as well.
-For one, the current accord concerning U.S. military bases in Greece lapses in May 1990.
-Another matter of concern is the extradition of Mohammed Rashid, a Palestinian terrorist who is wanted in the U.S. for the 1982 bombing of a Pan American Airways flight.
-The Greek courts have decided in favor of extradition in the Rashid case, but the matter awaits final approval from Greece's next justice minister.
-In recent years, U.S. steelmakers have supplied about 80% of the 100 million tons of steel used annually by the nation.
-Of the remaining 20% needed, the steel-quota negotiations allocate about 15% to foreign suppliers, with the difference supplied mainly by Canada -- which isn't included in the quota program.
-Other countries that don't have formal steel quotas with the U.S., such as Taiwan, Sweden and Argentina, also have supplied steel.
-Some of these countries have in recent years made informal agreements with the U.S. that are similar to quotas.
-Bus schedules were sometimes in disarray, stranding commuters such as Marilyn Sullivan.
-Her commute from Petaluma, Calif., normally takes an hour and 15 minutes, via the Golden Gate Bridge, which connects San Francisco with the North Bay area.
-But while traffic was heavy early in the commute over the Golden Gate, by 8 a.m. it already had thinned out.
-"It's one of the smoothest commutes I've ever had," said Charles Catania, an insurance broker on the bus from Mill Valley in Marin County.
-However, a spokeswoman for BankAmerica Corp. said yesterday's absenteeism at the bank holding company was no greater than on an average day.
-The Tax Court didn't believe that the Rubins, who earned $65,619 in their regular jobs, treated the sideline as a real business and derived "merely incidental elements of recreation and other personal pleasure and benefits" from it.
-The Direct Selling Association, a trade group, points out that its members, which include Amway Corp., cooperate with the IRS to distribute tax-compliance material to sales people and are helping to prepare a public-service television program on the subject.
-The independent-contractor project, which began in 1988, involves about 350 IRS agents.
-In the fiscal nine months ended June 30, reports Raymond P. Keenan, assistant commissioner for collection, they examined about 13,000 employers, assessed more than $67 million in delinquent employment taxes, and reclassified about 56,000 workers as employees instead of self-employed contractors.
-But many others, who want to qualify for employee benefits and unemployment compensation, become tipsters for the IRS, says Jerry Lackey, who manages the IRS project's force of nine agents in north and central Florida from Orlando.
-Retailers in Phoenix, Ariz., say P&G's new powdered detergent -- to be called Cheer with Color Guard -- will be on shelves in that market by early November.
-A P&G spokeswoman confirmed that shipments to Phoenix started late last month.
-The company introduced a superconcentrated Lemon Cheer in Japan after watching the success of Attack.
-When Attack hit the shelves in 1987, P&G's share of the Japanese market fell to about 8% from more than 20%.
-The fledgling science went corporate in 1977 when International Business Machines Corp. hired a marketing professor to help defend a complex antitrust case.
-The problem for IBM trial lawyers Thomas Barr and David Boies was how to make such a highly technical case understandable.
-Mr. Vinson, the professor, got the law bug and formed Litigation Sciences.
-(IBM won the case.)
-Mr. Stram said Enron is considering building gas-fired power plants in the U.K. capable of producing about 500 megawatts of power at a cost of about $300 million to $400 million.
-The timing of Quantum's chief executive officer, John Hoyt Stookey, appeared to be nothing less than inspired, because he had just increased Quantum's reliance on plastics.
-But now prices have nose-dived and Quantum's profit is plummeting.
-Through a venture with its investment banker, First Boston Corp., Quantum completed in August an acquisition of Petrolane Inc. in a transaction valued at $1.18 billion.
-Petrolane is the second-largest propane distributor in the U.S.
-The largest, Suburban Propane, was already owned by Quantum.
-About 400,000 commuters trying to find their way through the Bay area's quake-torn transportation system wedged cheek-to-jowl into subways, sat in traffic jams on major freeways or waited forlornly for buses yesterday.
-The massive temblor, which killed at least 61 people, severed the Bay Bridge, a major artery to the east, and closed most ramps leading to and from Highway 101, the biggest artery to the south.
-It will take several weeks to repair the bridge, and several months to repair some of the 101 connections.
-But in spite of a wind-driven rainstorm, gridlock never materialized, mainly because the Bay Area Rapid Transit subway system carried 50% more passengers than normal.
-UAL fell $6.25 a share to $191.75 on volume of 2.3 million shares in composite trading on the New York Stock Exchange as concern deepened among takeover stock traders about the length of time it will take to revive the purchase.
-Under the original buy-out approved by the UAL board Sept. 14, UAL's pilots planned to put up $200 million in cash and make $200 million in annual cost concessions for a 75% stake.
-UAL management was to pay $15 million for 10%, and British Air was to receive a 15% stake.
-The buy-out fell through when Citicorp and Chase Manhattan Corp. unexpectedly failed to obtain bank financing.
-Since then, UAL stock has fallen 33% in what may rank as the largest collapse of a takeover stock ever.
-If all the debt is converted to common, Automatic Data will issue about 3.6 million shares; last Monday, the company had nearly 73 million shares outstanding.
-Automatic Data is redeeming the bonds because the after-tax cost of the interest on the bonds is higher than the dividend yield on the common, a spokesman said.
-Dow Jones & Co. extended its tender offer of $18 a share, or about $576 million, for the 33% of Telerate Inc. that it doesn't already own until 5 p.m. EST, Nov. 6.
-The offer, which Telerate's two independent directors have rejected as inadequate, previously had been scheduled to expire at midnight Friday.
-Dow Jones said it extended the offer to allow shareholders time to review a supplement to the Dow Jones tender offer circular that it mailed last Friday.
-In any case, on the day of the meeting, Quantum's shares slid $2.625 to $36.625 in Big Board trading.
-On top of everything else, Quantum confronts a disaster at its plant in Morris, Ill.
-A prolonged production halt at the plant could introduce another imponderable into Quantum's financial future.
-When a plant has just been running flat out to meet demand, calculating lost profit and thus claims under business-interruption insurance is straightforward.
-Fulbright & Jaworski of Houston and Fenerty, Robertson, Fraser & Hatch of Calgary, Alberta, are affiliating to help serve their energy-industry clients.
-But they will work together on energy -, environmental - and fair-trade-related issues and conduct seminars on topics of mutual interest, said Gibson Gayle Jr. of 585-lawyer Fulbright & Jaworski.
-In addition, Fulbright & Jaworski's Washington, D.C., office will play a key role as the firms work together on regulatory issues, particularly natural-gas exports, for their clients.
-The arrangement, reached after about eight months of negotiations, grew out of 80-lawyer Fenerty Robertson's desire to develop ties with a U.S. firm in light of relaxed trade barriers between the U.S. and Canada, said Francis M. Saville of Fenerty Robertson.
-For one thing, Ms. Shere can draw on her cookbook, published by Random House four years ago, which is teeming with recipes for such specialties as kiwi sherbet, gooseberry fool (a creamy dish made with crushed stewed berries) and hazelnut "oeufs a la neige."
-"We make what we know how to make," says business manager Richard Mazzera.
-Many in the Bay Area's pastry community express disbelief that Ms. Shere kept only one copy of such valuable notes, but she has received moral support from Baker's Dozen, a group of California pastry chefs that meets regularly to discuss issues like how to keep meringues from weeping and how bovine eating habits affect butter texture.
-"Food manufacturer changes spelling of 'catsup' to 'ketchup,' saying that's the spelling people now prefer."
-In recent months the price of polyethylene, even more than that of other commodity plastics, has taken a dive.
-Meanwhile, the price of ethylene, the chemical building block of polyethylene, hasn't dropped nearly so fast.
-That discrepancy hurts Quantum badly, because its own plants cover only about half of its ethylene needs.
-China, which had been putting in huge orders for polyethylene, abruptly halted them.
-Slick graphics, pre-tested for effectiveness, also play a major role in Litigation Sciences' operation.
-They are very visually sophisticated, " explains LSI graphics specialist Robert Seltzer.
-"They may not have been able to articulate it all, but they did it," says Stephen Gillers, a legal ethics expert at New York University law school.
-Litigation Sciences concedes that in one in 20 cases it was flatout wrong in its predictions.
-A few attorneys offer horror stories of jobs botched by consultants or of overpriced services -- as when one lawyer paid a consultant (not at Litigation Sciences) $70,000 to interview a jury after a big trial and later read more informative interviews with the same jurors in The American Lawyer magazine.
-The latest period included the gain, which was $77 million before tax, from the previously announced sale of the institutional money management business of Lehman Management Co.
-The 1988 period was restated from net income of $8 million to correct an overstatement in the company's Boston Co. subsidiary.
-In the 1989 second quarter, Shearson had net income of $55 million, or 54 cents a share.
-In New York Stock Exchange composite trading yesterday, Shearson shares lost 37.5 cents to $18.125.
-The U.S. Export-Import Bank tentatively decided to guarantee commercial bank financing for the purchase of two Boeing Co. 767 airliners by Avianca, Colombia's international airline, at a cost of about $150 million.
-Mexico exported an average of 1,296,800 barrels of crude oil a day at an average of $15.31 a barrel during 1989's first eight months for a total of $4.82 billion, Petroleos Mexicanos S.A. said.
-New orders for durable goods fell back slightly in September after shooting up the month before, reflecting weakening auto demand after a spurt of orders for new 1990 models, the Commerce Department reported.
-That "suggests the manufacturing sector is not falling apart," said Sally Kleinman, an economist at Manufacturers Hanover Securities Corp. in New York.
-Orders for military goods usually catapult in September, government officials say, as the Pentagon scrambles to spend its money before the new fiscal year begins Oct. 1.
-While all the numbers in the durable goods report were adjusted for seasonal fluctuations, a Commerce Department analyst said that the adjustment probably didn't factor out all of the wide-ranging surge in defense orders.
-Gerald Maier, president and chief executive officer of the natural-gas pipeline and marketing concern, said the company's future growth is "increasingly linked" to decisions made by Calgary-based gas producers.
-"Since deregulation of the market in 1985, producers have become much more intensely involved in both transportation and marketing, " Mr. Maier said."
-TransCanada transports all gas that moves eastward from Alberta.
-Walter Litvinchuk, vice president of Pan-Alberta Gas Ltd., a Calgary-based gas marketing concern, said the industry will welcome the move.
-With regard to Greece's long-bubbling bank-looting scandal, Mr. Papandreou's principal accuser remains George Koskotas, former owner of the Bank of Crete and self-confessed embezzler, now residing in a jail cell in Salem, Mass., from where he is fighting extradition proceedings that would return him to Greece.
-Among unanswered questions are whether Mr. Papandreou received $23 million of stolen Bank of Crete funds and an additional $734,000 in bribes, as contended; whether the prime minister ordered state agencies to deposit some $57 million in Mr. Koskotas's bank and then skim off the interest; and, what PASOK's cut was from the $210 million Mr. Koskotas pinched.
-Two former ministers were so heavily implicated in the Koskotas affair that PASOK members of Parliament voted to refer them to the special court.
-Mr. Carpenter, a regional correspondent for National Review, has lived in Athens since 1981.
-A federal appeals court in San Francisco ruled that shareholders can't hold corporate officials liable for false sales projections on new products if the news media concurrently revealed substantial information about the product's flaws.
-The ruling stems from a 1984 suit filed by shareholders of Apple Computer Inc., claiming that company officials misled investors about the expected success of the Lisa computer, introduced in 1983.
-Boston Edison Co. said it will take a previously reported $60 million charge against earnings in the fourth quarter.
-The charge resulted from a settlement approved yesterday by the Massachusetts Department of Public Utilities.
-As expected, the settlement limits rate increases for three years and ties future charges to customers for operation of the troubled Pilgrim Nuclear Power Station to that plant's performance.
-Pilgrim had been closed for 32 months.
-Not a gripping question, unless you're the pastry chef of this city's Chez Panisse restaurant and you've just lost your priceless personal dessert notebook.
-A jury in 1986 agreed with the USFL's claims that the NFL monopolized major league football.
-But the jury awarded the USFL only $1 in damages, trebled because of the antitrust claims.
-Last week, the U.S. Court of Appeals in New York upheld a $5.5 million award of attorneys fees to the defunct league.
-Harvey D. Myerson, of Myerson & Kuhn, then of Finley, Kumble, Wagner, Heine, Underberg, Manley, Myerson & Casey, was the lead trial lawyer, and his new firm pursued the application appeal.
-Douglas R. Pappas of Myerson & Kuhn says about $5.3 million of the award goes directly to the USFL to reimburse it for fees already paid.

data/Seq2KG/cateringServices.txt

@@ -1,134 +0,0 @@
-Receiving a steady stream of unwanted text messages from some acquaintance to whom you foolishly gave your number is a true nightmare scenario.
-A man named Jonathan Anozie is living this nightmare, reports TMZ, and the offending creepster is Papa John.
-Well, it probably isn't real-life Papa John's founder John Schnatter sending the texts, but an automated marketing system for his pizza chain is apparently overloading Anozie's mobile notifications with offers for discounted pies.
-As such, the Beverly Hills, California, resident is suing the chain for $500 per unwanted text.
-The lawsuit, filed in the United States District Court Central District of California, claims Anozie replied "STOP" on multiple occasions, but the messages just kept coming.
-The alleged deluge caused the plaintiff "to suffer a significant amount of anxiety, frustration, and annoyance."
-Who among us hasn't experienced anxiety, frustration, and annoyance upon a plethora of unwanted texts?
-"I want this to be the unifying sushi that anyone can eat, but nobody wants to eat," says chef Francis, the proprietor of Kuko, Portland's only restaurant specializing in airport-style sushi.
-His goal is to serve the "most borderline not-sushi sushi in the world."
-He also wants to serve sushi that makes his guests wonder if they're "eating bits of plastic."
-The chef, played by Fred Armisen, was inspired to open his restaurant by a meal at the Denver airport, where he first discovered sushi with "a fishy, sweet-for-some-reason flavor" that crumbled in his hands.
-"I want to make it like we have no love for it," the chef explains.
-Francis is the star of Portlandia's hilarious Chef's Table parody, which references every stylistic trademark of David Gelb's hit Netflix series in under 90 seconds.
-This clip has everything: a candid origin story, shots of a chef walking through nature, a frenetic dinner service, and lots of intense classical music.
-Bravo, Portlandia:
-Customers were reporting upwards of three hour-long waits at some bakeries in Hamtramck this morning as patrons from from across the region gathered to take part in the annual Paczki Day tradition of stand and wait.
-While in past years Fat Tuesday has fallen in the midst of an extreme cold snap or snow storm, 2017's crowds lucked out with light rain showers and relatively mild temperatures.
-At New Martha Washington Bakery and New Palace Bakery lines snaked through shops, out the door, and clear down full city blocks.
-Inside bakery staff rushed to fold boxes, fill orders, and generally get the crush of customers out the door as quickly as possible.
-Eater photographers Michelle and Chris Gerard stopped by metro Detroit's traditional fried Polish pastry epicenter today to scope out the scene.
-Check out the insane morning rush photos in the gallery below.
-McDonald's latest endeavor may come as a bit of a surprise: The fast-food behemoth is pursuing sustainable beef.
-As Fortune reports, the chain is funding two sustainable beef pilot programs in the U.S., following years of tests in Canada, Europe, and Brazil.
-The first program involves a research partnership with agricultural nonprofit the Noble Foundation that will seek out ways in which sustainability can be improved across the entire U.S. beef supply chain.
-For the second program, McDonald's is putting up $4.5 million to test new cattle-grazing practices "that can actually lead to net-negative carbon impact," according to a statement from the company.
-McDonald's also says it will eliminate deforestation (the cutting down of forests to make room to raise cattle) from its supply chain by 2020.
-It's not all selfies and champagne showers over at Noma, the acclaimed Copenhagen restaurant that closed the doors to its original location a few days ago.
-As chef/owner Ren é Redzepi makes his plans for what the next iteration will bring, he has announced new partners in the restaurant: restaurant manager James Spreadbury, service director Lau Richter, and dishwasher Ali Sonko.
-The chef also plans to gift pieces of the walls of Noma 1.0 to various staff members.
-New partners: As we close the doors to the old noma, we also push towards the next rendition.
-We are almost positive we will open the doors to our new space at the end of this year.
-But, most importantly, we are here to tell you that noma in its new edition will have a handful of new partners.
-It gives me incredible joy to let the world know that our restaurant managers Lau and James, and our dishwasher, Ali, have become partners in noma.
-This is only the beginning, as we plan to surprise several more of our staff with a piece of the walls that they have chosen to work so hard within.
-This move is one of the happiest moments of my time at noma - best wishes Ren é Redzepi
-A financial analyst told Reuters expansion to the U.K. would be a "logical step" for Amazon.
-The company apparently employed the same survey strategy before debuting its delivery venture stateside: "These stealth tactics have been used carefully in the United States to do similar and launch successfully, and the U.K. is often used as the first international market," Neil Campling, a senior analyst at Aviate Global, told Reuters.
-The AP's report centers on a popular Iranian restaurant chain, Shayah, that has 13 locations in Saudi Arabia, mostly in the capital city of Riyadh.
-The Saudi-owned company originally employed Iranian chefs who taught their Saudi counterparts how to prepare Iranian dishes like saffron rice and lamb skewers, but now the restaurant's general manager says all its Iranian employees have left the country; these days, Iranians would be unable to obtain work visas.
-Sam Beall, the proprietor of Blackberry Farm in Walland, Tenn. (about 30 miles south of Knoxville), died late yesterday in a skiing accident in Colorado.
-Beall was 39.
-From a release: "The Beall family and the Blackberry Farm team are understandably shocked by this heartbreaking news about the man they loved dearly as a son, brother, father, friend and host.
-They welcome the thoughts and prayers of all those whose lives were touched by Sam's hospitable nature, visionary leadership and adventurous spirit.
-They also request privacy for the Beall family during this difficult time."
-Though he was far from a household name, Beall's presence in the food world was gentle but impactful.
-His father, Sandy Beall, founded Ruby Tuesday in 1972.
-In 1976, Sandy and his wife Kreis purchased Blackberry Farm and began renovations and redesigns in order to turn it into a luxury lodge and farm; it is today a designated member of the Relais & Chateaux fellowship.
-Germany has long taken pride in its beer industry, boasting a 500-year-old purity law that regulates what can and can't go into suds produced in the country.
-But it appears German beer might not be as pure as it seems.
-Traces of glyphosate, a widely used herbicide, have been found in the country's 14 most popular brews, Reuters reports.
-Glyphosate is the key ingredient in Roundup, a popular weed killer developed by American agrochemical company Monsanto.
-The Food and Drug Administration recently announced it would begin testing produce for the herbicide in certain types of produce because it's been found to be a possible carcinogen.
-Last March, experts at the World Health Organization concluded glyphosate "probably" causes cancer in humans.
-The Munich Environmental Institute, an activist and investigative group, discovered traces of the herbicide in the country's beer.
-But, industry and governmental organizations have pushed back on the findings.
-Germany's Federal Institute for Risk said the amount of glyphosate found does not pose a risk: "An adult would have to drink around 1,000 liters (264 U.S. gallons) of beer a day to ingest enough quantities to be harmful for health."
-The environmental group claims it found traces above the 0.1 microgram limit allowed in drinking water.
-From the studios of WNYC, Dan Pashman and Anne Noyes Saini produce The Sporkful, which, put simply, is a podcast about food.
-In a recently launched series called "Other People's Food," Pashman and a series of guests dig into what's currently a very hot topic in the food world: race, food, and cultural appropriation.
-In a city rife with foods from all cultures and countries, Pashman dives into issues that arise when people eat, cook, and change the food from a culture "they weren't born into."
-A previous episode of "Other People's Food" featured Chicago chef Rick Bayless, and the chef has drawn some major criticism for his comments on cooking Mexican food as a white man.
-The next episode of features actress Rosie Perez, an actress and activist who was born in New York to Puerto Rican parents.
-A burglar who broke into a Tennessee restaurant over the weekend left empty-handed, but at least they got their thirst quenched.
-The intruder's target was Tomato Head restaurant in Knoxville, as WBIR reports.
-The suspect forced open the restaurant's cash register only to find it empty, a rep for the Knoxville Police Department tells Eater via email; realizing he or she wasn't going to come away with any cash, the parched burglar apparently sought solace in a Dale's Pale Ale, imbibing in a can of the popular beer from Colorado-based brewery Oskar Blues before taking off.
-The thief clearly wasn't hungry, because nothing else was taken except for the beer, Knoxville PD says, and the cash register was the only thing disturbed.
-The unknown thief isn't the first to break and enter in search of sustenance: Some burger bandits in the UK broke into a soccer clubhouse and cooked themselves a meal, even leaving a note of thanks for the tasty treats (along with nearly $1,500 of damage) in their wake.
-In another case, a raccoon with an apparent thirst for booze broke into an alcohol storage warehouse and drank a little too much.
-London-based startup and major food delivery player Deliveroo just launched an intriguing new initiative: It's now providing kitchen space for its restaurant partners in an effort to serve more customers, reports TechCrunch.
-Called RooBox, the intention of the off-site kitchens is to "[bring] restaurant brands to areas of London that have a large residential population but are currently underserved in terms of available restaurants via the Deliveroo app."
-Deliveroo specializes in delivery from "premium" restaurants that wouldn't typically offer takeout, including at least one Michelin-starred restaurant.
-The company only delivers food within a 2 kilometer (1.25 mile) radius of each restaurant to ensure it arrives hot and fresh, but that means depending on where a customer lives, their options can be limited or even nonexistent.
-By providing restaurants with equipped kitchens in areas of London that aren't rife with restaurants — or at least, not the kind of restaurants Deliveroo partners with — the company can expand its customer base.
-General Mills has issued a major recall of products sold under its Gold Medal Flour label.
-The voluntary recall, announced Tuesday, covers 10 million pounds of flour, according to USA Today, and it's related to an E. coli outbreak that has sickened 38 people in 20 states.
-"As a leading provider of flour for 150 years, we felt it was important to not only recall the product and replace it for consumers if there was any doubt, but also to take this opportunity to remind our consumers how to safely handle flour," Liz Nordlie, president of General Mills baking division, said in a prepared statement.
-The company is working with health officials to investigate an outbreak of E. coli strain O121, which dates back to December.
-General Mills says the outbreak may be potentially connected to Gold Medal flour, Wondra flour, and Signature Kitchens flour, but so far E. coli has not been found in any of its products or in its flour-manufacturing facility in Kansas City, Mo.
-It's been a rough few months for Chipotle.
-A widespread E. coli outbreak sickened dozens of customers, and the burrito chain still hasn't been able to pinpoint what caused it; there was also that pesky norovirus disaster in Boston that made more than 100 diners ill. As the chain attempts to clean up its act and win customers back — and faces several lawsuits — it will shutter all its stores for a few hours on February 8 to talk to its employees about food safety.
-Miraculously, Late Night With Conan O'Brien managed to get its hands on a copy of Chipotle's "new training video," and it offers some insights into what may have gone so very wrong at the chain: Going forward, employees must "stop using rice scraped up from the steps of weddings," quit using tortillas to clean their car windshields, and perhaps most importantly, discontinue the use of germ-spreading "sneeze megaphones."
-If only things were that simple.
-Christine Flynn — Executive Chef at Toronto's iQ Food Co. — has quite an imagination... and, an alternate persona.
-Until today, she was perhaps more widely known as the Instagram celebrity Jacques La Merde.
-Poking fun at chef bros and anyone who takes themselves too seriously, Flynn created, photographed, a posted a photo of a carefully plated dish every few days.
-The dishes were always composed of ingredients found at fast food restaurants, corner stores, vending machines, or the junk food aisle.
-Eater has been trying to guess Flynn's identity for months, but tonight "the shit" hit the fan and all is revealed on Top Chef.
-Says Flynn in an email, "I joke about how great my b-rolodex has gotten this year, but actually, I'm more excited about building an incredible FEMPIRE!!!!!"
-Here's Eater's exclusive interview with the woman, the myth, the legend.
-In the dreary, dystopian future when brands rule the world, the best restaurant in America's dining capital of New York City might be run by PepsiCo.
-Or maybe that will happen later this year when the soft drink giant opens Kola House in the city's Chelsea neighborhood.
-Kola House.
-Pepsi is opening a New York restaurant called Kola House, reports the Times.
-Kola House.
-PepsiCo has always tried to separate itself from rival Coca-Cola by marketing to the most cutting edge of Americans.
-It's responsible for bringing Crystal Pepsi into this world, and a new restaurant appears to be the company's latest attempt to capture Generation Next.
-PepsiCo chief marketing officer Seth Kaufman told the Times, "This isn't a pop-up.
-This is something much bigger than that."
-The company hasn't decided on a menu or executive chef yet, but NYC bartender Alex Ott reportedly will consult on cocktails.
-Expect libations to be made with Caleb's Kola, PepsiCo's high-brow, millennial-targeting line of soda.
-There's no projected opening date yet, but it's on track to begin service this spring.
-Kola House won't be slapped with a bunch of Pepsi signage and memorabilia, but instead will include "a logo here or there, nothing too obvious."
-Levi's Stadium in Santa Clara, Calif., set to host Super Bowl 50 next Sunday, is the most state-of-the-art venue in the NFL, and it has the mobile app to match.
-Among its many features, the official app of the big game helps fans avoid the long lines often found at concession stands, writes Mobile Sports Report.
-Fans can place orders on their phones, before picking up their food and beverages at express windows around the stadium.
-The Super Bowl app, which incorporates features from the Levi's Stadium version, actually takes a step back.
-While it allows fans to order drinks and have them delivered directly to their seats, it doesn't allow food delivery, which is available when the San Francisco 49ers play their home games at the stadium.
-Still, it's a nice touch for impatient and thirsty fans who don't want to wait for the roaming beer vendor to reach their aisle.
-Having already created a restaurant based on the idea that people love hot sauce, iconic Louisiana brand Tabasco is going one step further.
-The McIlhenny Company, which produces the famous pepper sauce, is almost ready to launch its new museum, a spokesperson tells Eater.
-It will open next week adjacent to the company's restaurant and headquarters on Avery Island.
-Officially dubbed the Tabasco Sauce Visitors Center, the new venue "will feed fans' curiosity with an inside look into the world of Tabasco — from when the sauce was first created over a century ago, to how it's made today and how it has impacted the culinary world."
-The formal opening is scheduled for Tuesday, February 2.
-The McIlhenny Company opened its Tabasco-inspired restaurant, called 1868 (the year the company was founded), in August.
-The eatery and forthcoming museum are part of a major expansion to help celebrate the company's impending 150th anniversary.
-At 1868, every dish on the menu, unsurprisingly, contains Tabasco sauce.
-The cuisine is straight out of a Cajun and Creole cookbook — again, no surprise here.
-A Philadelphia-based food testing startup has developed a new technology called Veriflow to detect illness-causing pathogens in foods.
-Invisible Sentinel uses a small device designed to scan for the DNA of E. coli, salmonella, listeria, and other food-born microorganisms in order to quickly determine the safety of a food item, the New York Times reported.
-In recent months, Chipotle has come under fire for a widespread incidence of E. coli in its restaurants which caused dozens of illnesses (and spurred several lawsuits).
-Blue Bell Creameries has also struggled with listeria-related illnesses, and more recently, Dole recently recalled bagged salads after one person was killed and 12 were sickened by listeria.
-Incidents like these indicate a clear need for a solution so customers can avoid ill effects and companies can steer clear of PR nightmares, stock hits, and consequent complicated recovery plans.
-Since acclaimed New Nordic pioneer chef Ren é Redzepi announced he would be taking his Copenhagen restaurant, Noma, on the road for a 10-week pop up in Australia, the food world has been awaiting what was predicted to be a cutting-edge, unique, and — of course — hyperlocal menu.
-The success of the two Michelin star restaurant's previous pop-ups — Noma Tokyo ran for five weeks last year — has created a frenzy for food enthusiasts looking to snag a seat for the much-anticipated opening.
-At $339 USD per person, the pricey pop-up has not only sold out, but currently has 27,000 people on the waiting list.
-Debuting in the Sydney neighborhood of Barangaroo earlier this week, Noma Australia opened its doors with a menu inspired by the restaurant's harborside location.
-The coastally-driven dishes boast several varieties of oceanic plants and sea vegetables, as well as strawberry clams, sea urchin, and flame cockle.
-Produce items utilized include wild berries, lantana flowers, and lemon myrtle, while proteins include crocodile fat, local ants, and magpie goose.
-Get ready to consult your gastronomic dictionary; here are the dishes currently featured on the menu according to eager Instagrammers (all are subject to change before Noma Australia closes its doors on April 2).
-As America's finest presidential candidates criss-cross the country, one side is talking about inclusion while the other preaches a message of exclusion, and ideas of acceptance and discrimination are playing out in small, local, everyday ways.
-Earlier this week a woman in Richmond, Va., claims she was fired by a local KFC restaurant manager about an hour after being hired once the manager found out she was transgender.
-Georgia Carter contacted a local TV station in Richmond after she received a phone call from the manager telling her not to come in for training the following day.
-Carter told a local reporter the restaurant's management said they could not hire her because her driver's license identified her as a male, and they were not sure which bathroom she could use.
-In response to the allegations, and after an internal investigation, KFC's chief people officer John Kurnick released a statement to Eater:

data/openstax/OS_bio_4_2.txt

@@ -1,66 +0,0 @@
-A cell is the smallest unit of a living thing.
-Whether comprised of one cell (like bacteria) or many cells (like a human), we call it an organism.
-Thus, cells are the basic building blocks of all organisms.
-Several cells of one kind that interconnect with each other and perform a shared function form tissues.
-These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system).
-Several systems that function together form an organism (like a human being).
-Here, we will examine the structure and function of cells.
-There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic.
-For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic.
-Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, we will first examine how biologists study cells.
-Cells vary in size.
-With few exceptions, we cannot see individual cells with the naked eye, so scientists use microscopes (micro- = "small"; -scope = "to look at") to study them.
-A microscope is an instrument that magnifies an object.
-We photograph most cells with a microscope, so we can call these images micrographs.
-The optics of a microscope's lenses change the image orientation that the user sees.
-A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa.
-Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up.
-This occurs because microscopes use two sets of lenses to magnify the image.
-Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright).
-To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter.
-A pin head is about two thousandths of a meter (two mm) in diameter.
-That means about 250 red blood cells could fit on a pinhead.
-Most student microscopes are light microscopes (Figure 4.2a).
-Visible light passes and bends through the lens system to enable the user to see the specimen.
-Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains.
-Staining, however, usually kills the cells.
-Light microscopes that undergraduates commonly use in the laboratory magnify up to approximately 400 times.
-Two parameters that are important in microscopy are magnification and resolving power.
-Magnification is the process of enlarging an object in appearance.
-Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail.
-When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times.
-In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes.
-a) Most light microscopes in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers.
-b) Electron microscopes provide a much higher magnification, 100,000x, and a have a resolution of 50 picometers.
-use a beam of electrons instead of a beam of light.
-Not only does this allow for higher magnification and, thus, more detail (Figure 4.3), it also provides higher resolving power.
-The method to prepare the specimen for viewing with an electron microscope kills the specimen.
-Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope.
-In a scanning electron microscope, a beam of electrons moves back and forth across a cell's surface, creating details of cell surface characteristics.
-In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell's internal structures.
-As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes.
-a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope.
-b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow).
-Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail.
-For another perspective on cell size, try the HowBig interactive at this site.
-The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s.
-Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed "animalcules."
-In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term "cell" for the box-like structures he observed when viewing cork tissue through a lens.
-In the 1670s, van Leeuwenhoek discovered bacteria and protozoa.
-Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells.
-By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells.
-Rudolf Virchow later made important contributions to this theory.
-Have you ever heard of a medical test called a Pap smear (Figure 4.4)?
-In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection.
-Cytotechnologists (cyto- = "cell") are professionals who study cells via microscopic examinations and other laboratory tests.
-They are trained to determine which cellular changes are within normal limits and which are abnormal.
-Their focus is not limited to cervical cells.
-They study cellular specimens that come from all organs.
-When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause.
-Cytotechnologists play a vital role in saving people's lives.
-When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome.
-These uterine cervix cells, viewed through a light microscope, are from a Pap smear.
-Normal cells are on the left.
-The cells on the right are infected with human papillomavirus (HPV).
-Notice that the infected cells are larger.
-Also, two of these cells each have two nuclei instead of one, the normal number.

main.py

@@ -1,5 +1,9 @@
+import json
 import os
+import secrets
+import string
 from datetime import datetime
+from zipfile import ZipFile
 
 import gradio as gr
 import pandas as pd
@@ -7,11 +11,12 @@ from langchain.chains import SimpleSequentialChain
 from langchain.chat_models import ChatOpenAI
 from nltk.tokenize import sent_tokenize
 
+import utils
 from chains import chains
-from process import process
 
 
 class Text2KG:
+    """Text2KG class."""
 
     def __init__(self, api_key: str, **kwargs):
 
@@ -19,27 +24,53 @@ class Text2KG:
 
     
     def init_pipeline(self, *steps: str):
+        """Initialize Text2KG pipeline from passed steps.
+        
+        Args:
+            *steps (str): Steps to include in pipeline. Must be a top-level name present in
+                the schema.yml file
+        """
         self.pipeline = SimpleSequentialChain(
             chains=[chains[step](llm=self.model) for step in steps],
             verbose=False
         )
 
     
-    def run(self, text: str):
+    def run(self, text: str) -> list[dict]:
+        """Run Text2KG pipeline on passed text.
+        
+        Arg:
+            text (str): The text input
+        
+        Returns:
+            triplets (list): The list of extracted KG triplets
+        """
         triplets = self.pipeline.run(text)
 
-        [triplet.update({"context": text}) for triplet in triplets]
-
-        return  triplets
+        return triplets
 
 
 def create_knowledge_graph(api_key: str, ngram_size: int, axiomatize: bool, text: str, progress=gr.Progress()):
-
+    """Create knowledge graph from text.
+    
+    Args:
+        api_key (str): OpenAI API key
+        ngram_size (int): Number of sentences per forward pass
+        axiomatize (bool): Whether to decompose sentences into simpler axioms as 
+            a pre-processing step. Doubles the amount of calls to ChatGPT
+        text (str): Text from which Text2KG will extract knowledge graph from
+        progress: Progress bar. The default is gradio's progress bar; for a 
+            command line progress bar, set `progress = tqdm`
+
+    Returns:
+        knowledge_graph (DataFrame): The extracted knowledge graph
+        zip_path (str): Path to ZIP archive containing outputs
+    """
     # init
     if api_key == "":
         raise ValueError("API key is required")
     
-    model = Text2KG(api_key=api_key, temperature=0.3)
+    model = Text2KG(api_key=api_key, temperature=0.3) # low temp. -> low randomness
 
     if axiomatize:
         steps  = ["text2axiom", "extract_triplets"]
@@ -56,27 +87,61 @@ def create_knowledge_graph(api_key: str, ngram_size: int, axiomatize: bool, text
     # create KG
     knowledge_graph = []
     
-    for ngram in progress.tqdm(ngrams, desc="Processing..."):
+    for i, ngram in progress.tqdm(enumerate(ngrams), desc="Processing...", total=len(ngrams)):
         output = model.run(ngram)
+        [triplet.update({"sentence_id": i}) for triplet in output]
+
         knowledge_graph.extend(output)
 
-    knowledge_graph = pd.DataFrame(knowledge_graph)
-    knowledge_graph = process(knowledge_graph)
 
+    # convert to df, post-process data
+    knowledge_graph = pd.DataFrame(knowledge_graph)
+    knowledge_graph = utils.process(knowledge_graph)
+    
+    # rearrange columns
+    knowledge_graph = knowledge_graph[["sentence_id", "subject", "relation", "object"]]
 
+    # metadata
     now = datetime.now()
     date = str(now.date())
     timestamp = now.strftime("%Y%m%d%H%M%S")
+
+    metadata = {
+        "timestamp": timestamp,
+        "batch_size": ngram_size,
+        "axiom_decomposition": axiomatize
+    }
+
+    # unique identifier for saving
+    uid = ''.join(secrets.choice(string.ascii_letters)
+                  for _ in range(6))
     
-    path = os.path.join(".", "output", date)
-    os.makedirs(path, exist_ok=True)
+    save_dir = os.path.join(".", "output", date, uid)
+    os.makedirs(save_dir, exist_ok=True)
+
+
+    # save metadata & data
+    with open(os.path.join(save_dir, "metadata.json"), 'w') as f:
+        json.dump(metadata, f)
     
-    filename = f"kg-{timestamp}--batch-{ngram_size}--axiom-{axiomatize}.csv"
-    filepath = os.path.join(path, filename)
+    ngrams_df = pd.DataFrame(enumerate(ngrams), columns=["sentence_id", "text"])
+    ngrams_df.to_csv(os.path.join(save_dir, "sentences.txt"), 
+                     index=False)
+
+    knowledge_graph.to_csv(os.path.join(save_dir, "kg.txt"), 
+                           index=False)    
+    
+
+    # create ZIP file
+    zip_path = os.path.join(save_dir, "output.zip")
+
+    with ZipFile(zip_path, 'w') as zipObj:
 
-    knowledge_graph.to_csv(filepath, index=False)
+        zipObj.write(os.path.join(save_dir, "metadata.json"))
+        zipObj.write(os.path.join(save_dir, "sentences.txt"))
+        zipObj.write(os.path.join(save_dir, "kg.txt"))
 
-    return knowledge_graph, filepath
+    return knowledge_graph, zip_path
 
 
 class App:
@@ -90,19 +155,30 @@ class App:
             fn=create_knowledge_graph,
             description=description,
             inputs=[
-                gr.Textbox(placeholder="API key...", label="OpenAI API Key"),
-                gr.Slider(maximum=10, step=1, label="Batching", info="Number of sentences per batch? (0 = do not chunk text)", ),
-                gr.Checkbox(label="Axiomatize", info="Decompose sentences into simpler axioms?\n(ex: \"I like cats and dogs.\" = \"I like cats. I like dogs.\")"),
+                gr.Textbox(placeholder="API key...", label="OpenAI API Key", type="password"),
+                gr.Slider(maximum=10, step=1, label="Sentence Batching", info="Number of sentences per forward pass? Affects the number of calls made to ChatGPT.", ),
+                gr.Checkbox(label="Axiom Decomposition", info="Decompose sentences into simpler axioms?\n(ex: \"I like cats and dogs.\" = \"I like cats. I like dogs.\")\nDoubles the number of calls to ChatGPT."),
                 gr.Textbox(lines=2, placeholder="Text Here...", label="Input Text"),
             ],
             outputs=[
                 gr.DataFrame(label="Knowledge Graph Triplets", 
-                             headers=["subject", "relation", "object", "context"], 
+                             headers=["sentence_id", "subject", "relation", "object"], 
                              max_rows=10, 
                              overflow_row_behaviour="show_ends"),
                 gr.File(label="Knowledge Graph")
             ],
-            examples=[["", 1, True, description]],
+            examples=[["", 1, False, ("All cells share four common components: "
+                                        "1) a plasma membrane, an outer covering that separates the "
+                                        "cell's interior from its surrounding environment; 2) cytoplasm, "
+                                        "consisting of a jelly-like cytosol within the cell in which "
+                                        "there are other cellular components; 3) DNA, the cell's genetic "
+                                        "material; and 4) ribosomes, which synthesize proteins. However, "
+                                        "prokaryotes differ from eukaryotic cells in several ways. A "
+                                        "prokaryote is a simple, mostly single-celled (unicellular) "
+                                        "organism that lacks a nucleus, or any other membrane-bound "
+                                        "organelle. We will shortly come to see that this is significantly "
+                                        "different in eukaryotes. Prokaryotic DNA is in the cell's central "
+                                        "part: the nucleoid.")]],
             allow_flagging="never"
         )
         demo.queue(concurrency_count=10).launch(share=False)

output/2023-09-17/124439-200937_axiomatized.csv

@@ -1,147 +0,0 @@
-subject,relation,object,context
-cell,is,smallest unit of a living thing,"A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a human), we call it an organism. Thus, cells are the basic building blocks of all organisms."
-bacteria,comprised of,one cell,"A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a human), we call it an organism. Thus, cells are the basic building blocks of all organisms."
-human,comprised of,many cells,"A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a human), we call it an organism. Thus, cells are the basic building blocks of all organisms."
-organism,called,it,"A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a human), we call it an organism. Thus, cells are the basic building blocks of all organisms."
-cells,are,basic building blocks of all organisms,"A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a human), we call it an organism. Thus, cells are the basic building blocks of all organisms."
-cells,interconnect with,each other,"Several cells of one kind that interconnect with each other and perform a shared function form tissues. These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-cells,perform,shared function,"Several cells of one kind that interconnect with each other and perform a shared function form tissues. These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-tissues,formed by,combination of interconnected cells,"Several cells of one kind that interconnect with each other and perform a shared function form tissues. These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-organs,formed by,combination of tissues,"Several cells of one kind that interconnect with each other and perform a shared function form tissues. These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-organs,such as,"stomach, heart, or brain","Several cells of one kind that interconnect with each other and perform a shared function form tissues. These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-organ system,comprised of,several organs,"Several cells of one kind that interconnect with each other and perform a shared function form tissues. These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-organ system,such as,"digestive system, circulatory system, or nervous system","Several cells of one kind that interconnect with each other and perform a shared function form tissues. These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-organism,formed by,several systems,"Several cells of one kind that interconnect with each other and perform a shared function form tissues. These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-organism,example of,human being,"Several cells of one kind that interconnect with each other and perform a shared function form tissues. These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-structure,of,cells,"Here, we will examine the structure and function of cells. There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic. For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic."
-function,of,cells,"Here, we will examine the structure and function of cells. There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic. For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic."
-cells,are classified as,prokaryotic,"Here, we will examine the structure and function of cells. There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic. For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic."
-cells,are classified as,eukaryotic,"Here, we will examine the structure and function of cells. There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic. For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic."
-animal cells,are classified as,eukaryotic cells,"Here, we will examine the structure and function of cells. There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic. For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic."
-plant cells,are classified as,eukaryotic cells,"Here, we will examine the structure and function of cells. There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic. For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic."
-bacterial cells,are classified as,prokaryotic cells,"Here, we will examine the structure and function of cells. There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic. For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic."
-Cells,vary in,size,"Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, we will first examine how biologists study cells. Cells vary in size. With few exceptions, we cannot see individual cells with the naked eye, so scientists use microscopes (micro- = ""small""; -scope = ""to look at"") to study them."
-We,cannot see,individual cells with the naked eye,"Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, we will first examine how biologists study cells. Cells vary in size. With few exceptions, we cannot see individual cells with the naked eye, so scientists use microscopes (micro- = ""small""; -scope = ""to look at"") to study them."
-Scientists,use,microscopes to study cells,"Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, we will first examine how biologists study cells. Cells vary in size. With few exceptions, we cannot see individual cells with the naked eye, so scientists use microscopes (micro- = ""small""; -scope = ""to look at"") to study them."
-microscope,is,instrument,"A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs. The optics of a microscope's lenses change the image orientation that the user sees."
-microscope,magnifies,object,"A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs. The optics of a microscope's lenses change the image orientation that the user sees."
-we,photograph,cells,"A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs. The optics of a microscope's lenses change the image orientation that the user sees."
-cells,taken with,microscope,"A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs. The optics of a microscope's lenses change the image orientation that the user sees."
-images,called,micrographs,"A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs. The optics of a microscope's lenses change the image orientation that the user sees."
-microscope's lenses,change,image orientation,"A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs. The optics of a microscope's lenses change the image orientation that the user sees."
-user,sees,image orientation,"A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs. The optics of a microscope's lenses change the image orientation that the user sees."
-specimen,appear,upside-down,"A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa. Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image."
-specimen,appear,facing left,"A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa. Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image."
-microscope slide,view through,microscope,"A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa. Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image."
-microscope slide,move left,appear to move right,"A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa. Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image."
-microscope slide,move down,seem to move up,"A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa. Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image."
-microscopes,use,two sets of lenses,"A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa. Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image."
-lenses,magnify,image,"A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa. Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image."
-two lens system,produces,inverted image,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter. A pin head is about two thousandths of a meter (two mm) in diameter."
-binocular or dissecting microscopes,work in,similar manner,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter. A pin head is about two thousandths of a meter (two mm) in diameter."
-binocular or dissecting microscopes,include,additional magnification system,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter. A pin head is about two thousandths of a meter (two mm) in diameter."
-additional magnification system,makes,final image appear upright,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter. A pin head is about two thousandths of a meter (two mm) in diameter."
-typical human red blood cell,is about,eight millionths of a meter in diameter,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter. A pin head is about two thousandths of a meter (two mm) in diameter."
-typical human red blood cell,is about,eight micrometers in diameter,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter. A pin head is about two thousandths of a meter (two mm) in diameter."
-pin head,is about,two thousandths of a meter in diameter,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter. A pin head is about two thousandths of a meter (two mm) in diameter."
-pin head,is about,two mm in diameter,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter. A pin head is about two thousandths of a meter (two mm) in diameter."
-250 red blood cells,could fit on,a pinhead,That means about 250 red blood cells could fit on a pinhead. Most student microscopes are light microscopes (Figure 4.2a). Visible light passes and bends through the lens system to enable the user to see the specimen.
-student microscopes,are,light microscopes,That means about 250 red blood cells could fit on a pinhead. Most student microscopes are light microscopes (Figure 4.2a). Visible light passes and bends through the lens system to enable the user to see the specimen.
-Figure 4.2a,is,a light microscope,That means about 250 red blood cells could fit on a pinhead. Most student microscopes are light microscopes (Figure 4.2a). Visible light passes and bends through the lens system to enable the user to see the specimen.
-Visible light,passes and bends through,the lens system,That means about 250 red blood cells could fit on a pinhead. Most student microscopes are light microscopes (Figure 4.2a). Visible light passes and bends through the lens system to enable the user to see the specimen.
-the lens system,enables,the user to see the specimen,That means about 250 red blood cells could fit on a pinhead. Most student microscopes are light microscopes (Figure 4.2a). Visible light passes and bends through the lens system to enable the user to see the specimen.
-Light microscopes,are advantageous for,viewing living organisms,"Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells. Light microscopes that undergraduates commonly use in the laboratory magnify up to approximately 400 times."
-Individual cells,are generally,transparent,"Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells. Light microscopes that undergraduates commonly use in the laboratory magnify up to approximately 400 times."
-Components of transparent cells,are not distinguishable unless they are colored with,special stains,"Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells. Light microscopes that undergraduates commonly use in the laboratory magnify up to approximately 400 times."
-Staining,usually kills,cells,"Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells. Light microscopes that undergraduates commonly use in the laboratory magnify up to approximately 400 times."
-Light microscopes,commonly used by undergraduates in the laboratory,magnify up to approximately 400 times.,"Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells. Light microscopes that undergraduates commonly use in the laboratory magnify up to approximately 400 times."
-Magnification,is,an important parameter in microscopy,"Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-Resolving power,is,another important parameter in microscopy,"Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-Magnification,is,the process of enlarging an object in appearance,"Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-Resolving power,refers to,the microscope's ability to distinguish two adjacent structures as separate,"Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-The resolution,is,higher,"Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-The resolution,improves,the image's clarity and detail,"Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-oil immersion lenses,are used to study,small objects,"When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes. a) Most light microscopes in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers."
-magnification,increases to,"1,000 times","When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes. a) Most light microscopes in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers."
-scientists,typically use,electron microscopes,"When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes. a) Most light microscopes in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers."
-light microscopes,in a college biology lab,can magnify cells up to,"When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes. a) Most light microscopes in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers."
-light microscopes,in a college biology lab,have a resolution of,"When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes. a) Most light microscopes in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers."
-Electron microscopes,provide,much higher magnification,"b) Electron microscopes provide a much higher magnification, 100,000x, and a have a resolution of 50 picometers. use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 4.3), it also provides higher resolving power."
-Electron microscopes,have,a resolution of 50 picometers,"b) Electron microscopes provide a much higher magnification, 100,000x, and a have a resolution of 50 picometers. use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 4.3), it also provides higher resolving power."
-Electron microscopes,use,a beam of electrons instead of a beam of light,"b) Electron microscopes provide a much higher magnification, 100,000x, and a have a resolution of 50 picometers. use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 4.3), it also provides higher resolving power."
-Using a beam of electrons,allows for,higher magnification and more detail,"b) Electron microscopes provide a much higher magnification, 100,000x, and a have a resolution of 50 picometers. use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 4.3), it also provides higher resolving power."
-Using a beam of electrons,provides,higher resolving power,"b) Electron microscopes provide a much higher magnification, 100,000x, and a have a resolution of 50 picometers. use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 4.3), it also provides higher resolving power."
-method,kills,specimen,"The method to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope. In a scanning electron microscope, a beam of electrons moves back and forth across a cell's surface, creating details of cell surface characteristics."
-electrons,have,short wavelengths,"The method to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope. In a scanning electron microscope, a beam of electrons moves back and forth across a cell's surface, creating details of cell surface characteristics."
-electrons,move best in,vacuum,"The method to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope. In a scanning electron microscope, a beam of electrons moves back and forth across a cell's surface, creating details of cell surface characteristics."
-electron microscope,cannot view,living cells,"The method to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope. In a scanning electron microscope, a beam of electrons moves back and forth across a cell's surface, creating details of cell surface characteristics."
-scanning electron microscope,moves back and forth across,cell's surface,"The method to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope. In a scanning electron microscope, a beam of electrons moves back and forth across a cell's surface, creating details of cell surface characteristics."
-beam of electrons,creates,details of cell surface characteristics,"The method to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope. In a scanning electron microscope, a beam of electrons moves back and forth across a cell's surface, creating details of cell surface characteristics."
-transmission electron microscope,is,a type of microscope,"In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell's internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes. a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope."
-electron beam,penetrates,the cell,"In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell's internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes. a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope."
-electron beam,provides details of,a cell's internal structures,"In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell's internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes. a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope."
-electron microscopes,are,significantly more bulky and expensive than light microscopes,"In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell's internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes. a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope."
-Salmonella bacteria,appear as,tiny purple dots,"In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell's internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes. a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope."
-Salmonella bacteria,can be viewed with,a light microscope,"In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell's internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes. a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope."
-Salmonella bacteria,can invade,human cells,"b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail. For another perspective on cell size, try the HowBig interactive at this site."
-scanning electron microscope micrograph,shows,Salmonella bacteria in red,"b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail. For another perspective on cell size, try the HowBig interactive at this site."
-scanning electron microscope micrograph,shows,human cells in yellow,"b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail. For another perspective on cell size, try the HowBig interactive at this site."
-subfigure (b),shows,a different Salmonella specimen than subfigure (a),"b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail. For another perspective on cell size, try the HowBig interactive at this site."
-there,is,a comparative increase in magnification and detail between the two subfigures,"b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail. For another perspective on cell size, try the HowBig interactive at this site."
-HowBig interactive,provides,another perspective on cell size,"b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail. For another perspective on cell size, try the HowBig interactive at this site."
-HowBig interactive at a specific site,provides,another perspective on cell size,"b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail. For another perspective on cell size, try the HowBig interactive at this site."
-microscopes,are,complex,"The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-Antony van Leeuwenhoek,used,microscopes,"The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-Antony van Leeuwenhoek,was skilled in,crafting lenses,"The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-Antony van Leeuwenhoek,observed,movements,"The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-Antony van Leeuwenhoek,observed,single-celled organisms,"The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-Antony van Leeuwenhoek,termed,single-celled organisms,"The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-Robert Hooke,coined,term,"The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-Robert Hooke,observed,structures,"The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-Robert Hooke,viewing,cork tissue,"The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-cork tissue,viewing through,lens,"The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-van Leeuwenhoek,discovered,bacteria,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells."
-van Leeuwenhoek,discovered,protozoa,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells."
-"advances in lenses, microscope construction, and staining techniques",enabled,scientists to see some components inside cells,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells."
-Matthias Schleiden,studying,tissues,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells."
-Theodor Schwann,studying,tissues,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells."
-Matthias Schleiden and Theodor Schwann,proposed,unified cell theory,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells."
-unified cell theory,states,one or more cells comprise all living things,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells."
-unified cell theory,states,the cell is the basic unit of life,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells."
-unified cell theory,states,new cells arise from existing cells,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells."
-Rudolf Virchow,made contributions to,a theory,"Rudolf Virchow later made important contributions to this theory. Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-Pap smear test,is called,a medical test,"Rudolf Virchow later made important contributions to this theory. Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-doctor,takes,a small sample of cells from the patient's uterine cervix,"Rudolf Virchow later made important contributions to this theory. Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-sample,is sent to,a medical lab,"Rudolf Virchow later made important contributions to this theory. Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-cytotechnologist,stains,the cells,"Rudolf Virchow later made important contributions to this theory. Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-cytotechnologist,examines,the cells for any changes,"Rudolf Virchow later made important contributions to this theory. Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-changes,could indicate,cervical cancer,"Rudolf Virchow later made important contributions to this theory. Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-changes,could indicate,a microbial infection,"Rudolf Virchow later made important contributions to this theory. Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-Cytotechnologists,study,cells,"Cytotechnologists (cyto- = ""cell"") are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal. Their focus is not limited to cervical cells."
-Cytotechnologists,perform,microscopic examinations,"Cytotechnologists (cyto- = ""cell"") are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal. Their focus is not limited to cervical cells."
-Cytotechnologists,perform,other laboratory tests,"Cytotechnologists (cyto- = ""cell"") are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal. Their focus is not limited to cervical cells."
-Cytotechnologists,are trained to determine,which cellular changes are within normal limits,"Cytotechnologists (cyto- = ""cell"") are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal. Their focus is not limited to cervical cells."
-Cytotechnologists,are trained to determine,which cellular changes are abnormal,"Cytotechnologists (cyto- = ""cell"") are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal. Their focus is not limited to cervical cells."
-The focus of cytotechnologists,is not limited to,cervical cells,"Cytotechnologists (cyto- = ""cell"") are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal. Their focus is not limited to cervical cells."
-Cellular specimens,come from,organs,"They study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-Abnormalities,are noticed in,cellular specimens,"They study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-Cellular specimens,are studied by,pathologist,"They study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-Abnormalities,are noticed by,pathologist,"They study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-Pathologist,is,medical doctor,"They study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-Pathologist,is consulted when,abnormalities are noticed,"They study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-Pathologist,interprets and diagnoses,changes caused by disease in body tissue and fluids,"They study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-Disease in body tissue and fluids,cause,changes,"They study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-Cytotechnologists,play a vital role in,saving people's lives,"They study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-doctors,discover,abnormalities,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear. Normal cells are on the left."
-abnormalities,can begin,treatment,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear. Normal cells are on the left."
-treatment,usually increases,chances,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear. Normal cells are on the left."
-chances,of a successful outcome,,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear. Normal cells are on the left."
-uterine cervix cells,viewed through,light microscope,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear. Normal cells are on the left."
-uterine cervix cells,are from,Pap smear,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear. Normal cells are on the left."
-cells,are on,left,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear. Normal cells are on the left."
-cells,are,normal,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear. Normal cells are on the left."
-cells,are infected with,human papillomavirus (HPV),"The cells on the right are infected with human papillomavirus (HPV). Notice that the infected cells are larger. Also, two of these cells each have two nuclei instead of one, the normal number."
-infected cells,are larger,,"The cells on the right are infected with human papillomavirus (HPV). Notice that the infected cells are larger. Also, two of these cells each have two nuclei instead of one, the normal number."
-cells,have,two nuclei instead of one,"The cells on the right are infected with human papillomavirus (HPV). Notice that the infected cells are larger. Also, two of these cells each have two nuclei instead of one, the normal number."
-two of these cells,each have,two nuclei instead of one,"The cells on the right are infected with human papillomavirus (HPV). Notice that the infected cells are larger. Also, two of these cells each have two nuclei instead of one, the normal number."
-nuclei,are,the normal number,"The cells on the right are infected with human papillomavirus (HPV). Notice that the infected cells are larger. Also, two of these cells each have two nuclei instead of one, the normal number."

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-subject,relation,object,context
-cell,the smallest unit of,living thing,"A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a human), we call it an organism."
-bacteria,comprised of,one cell,"A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a human), we call it an organism."
-organism,comprised of,many cells,"A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a human), we call it an organism."
-human,an,organism,"A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a human), we call it an organism."
-cells,are,building blocks of organisms,"Thus, cells are the basic building blocks of all organisms. Several cells of one kind that interconnect with each other and perform a shared function form tissues."
-cells,interconnect with,each other,"Thus, cells are the basic building blocks of all organisms. Several cells of one kind that interconnect with each other and perform a shared function form tissues."
-cells,perform,shared function,"Thus, cells are the basic building blocks of all organisms. Several cells of one kind that interconnect with each other and perform a shared function form tissues."
-cells,form,tissues,"Thus, cells are the basic building blocks of all organisms. Several cells of one kind that interconnect with each other and perform a shared function form tissues."
-tissues,combine to form,organ,"These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-organs,comprise,organ system,"These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-"digestive system, circulatory system, and nervous system",examples of,organ systems,"These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-several systems,form,organism,"These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being)."
-scientists,group,cells,"Here, we will examine the structure and function of cells. There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic."
-cells,grouped into,categories,"Here, we will examine the structure and function of cells. There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic."
-categories,are,prokaryotic and eukaryotic,"Here, we will examine the structure and function of cells. There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic."
-animal cells,classified as,eukaryotic cells,"For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, we will first examine how biologists study cells."
-plant cells,classified as,eukaryotic cells,"For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, we will first examine how biologists study cells."
-bacterial cells,classified as,prokaryotic cells,"For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, we will first examine how biologists study cells."
-biologists,study,cells,"For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, we will first examine how biologists study cells."
-cells,vary in,size,"Cells vary in size. With few exceptions, we cannot see individual cells with the naked eye, so scientists use microscopes (micro- = ""small""; -scope = ""to look at"") to study them."
-scientists,use,microscopes to study cells,"Cells vary in size. With few exceptions, we cannot see individual cells with the naked eye, so scientists use microscopes (micro- = ""small""; -scope = ""to look at"") to study them."
-microscope,is,instrument,"A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs."
-microscope,magnifies,object,"A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs."
-cells,photographed with,microscope,"A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs."
-images,called,micrographs,"A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs."
-optics,change,image orientation,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-lenses,of microscope's,change image orientation,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-user,sees,image orientation,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-specimen,is,right-side up,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-specimen,is,facing right,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-microscope slide,has,specimen,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-one,views through,microscope,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-specimen,appears,upside-down,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-specimen,appears,facing left,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-specimen,is,upside-down,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-specimen,is,facing left,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-microscope,has,lenses,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-one,views through,microscope,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-specimen,appears,right-side up,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-specimen,appears,facing right,"The optics of a microscope's lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa."
-slide,move left,appear to move right,"Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image."
-slide,move down,seem to move up,"Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image."
-microscopes,use,two sets of lenses,"Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image."
-microscopes,magnify,image,"Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image."
-two lens system,produces,inverted image,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter."
-binocular or dissecting microscopes,work in,similar manner,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter."
-binocular or dissecting microscopes,produce,inverted image,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter."
-binocular or dissecting microscopes,include,additional magnification system,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter."
-additional magnification system,makes,final image appear upright,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter."
-typical human red blood cell,about,eight millionths of a meter in diameter,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter."
-typical human red blood cell,about,eight micrometers in diameter,"Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter."
-pin head,about,two thousandths of a meter in diameter,A pin head is about two thousandths of a meter (two mm) in diameter. That means about 250 red blood cells could fit on a pinhead.
-pin head,about,two mm in diameter,A pin head is about two thousandths of a meter (two mm) in diameter. That means about 250 red blood cells could fit on a pinhead.
-250 red blood cells,could fit on,pin head,A pin head is about two thousandths of a meter (two mm) in diameter. That means about 250 red blood cells could fit on a pinhead.
-student microscopes,are,light microscopes,Most student microscopes are light microscopes (Figure 4.2a). Visible light passes and bends through the lens system to enable the user to see the specimen.
-visible light,passes through,lens system,Most student microscopes are light microscopes (Figure 4.2a). Visible light passes and bends through the lens system to enable the user to see the specimen.
-visible light,bends through,lens system,Most student microscopes are light microscopes (Figure 4.2a). Visible light passes and bends through the lens system to enable the user to see the specimen.
-lens system,enables,user to see specimen,Most student microscopes are light microscopes (Figure 4.2a). Visible light passes and bends through the lens system to enable the user to see the specimen.
-user,sees,specimen,Most student microscopes are light microscopes (Figure 4.2a). Visible light passes and bends through the lens system to enable the user to see the specimen.
-light microscopes,advantageous for,viewing living organisms,"Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells."
-individual cells,generally,transparent,"Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells."
-components of cells,not distinguishable unless,they are colored with special stains,"Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells."
-staining,usually kills,cells,"Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells."
-light microscopes,commonly used in,laboratory,Light microscopes that undergraduates commonly use in the laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power.
-light microscopes,can magnify up to,approximately 400 times,Light microscopes that undergraduates commonly use in the laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power.
-magnification,an important parameter in,microscopy,Light microscopes that undergraduates commonly use in the laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power.
-resolving power,an important parameter in,microscopy,Light microscopes that undergraduates commonly use in the laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power.
-magnification,is,process,"Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-magnification,enlarges,object,"Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-object,has appearance,enlarged,"Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-resolving power,is,ability,"Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-microscope,has resolving power,distinguish two adjacent structures,"Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-two adjacent structures,distinguished as separate,by microscope,"Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-resolution,is,higher,"Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-higher resolution,improves,image's clarity,"Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-higher resolution,improves,image's detail,"Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-image,has clarity,improved by higher resolution,"Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-image,has detail,improved by higher resolution,"Magnification is the process of enlarging an object in appearance. Resolving power is the microscope's ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image's clarity and detail."
-one,uses,oil immersion lenses,"When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes."
-oil immersion lenses,study,small objects,"When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes."
-magnification,increases to,"1,000 times","When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes."
-scientists,use,electron microscopes,"When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes."
-electron microscopes,typically use,gain a better understanding of cellular structure and function,"When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes."
-light microscopes,can magnify,cells up to approximately 400 times,"a) Most light microscopes in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers. b) Electron microscopes provide a much higher magnification, 100,000x, and a have a resolution of 50 picometers."
-light microscopes,have a resolution of,about 200 nanometers,"a) Most light microscopes in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers. b) Electron microscopes provide a much higher magnification, 100,000x, and a have a resolution of 50 picometers."
-electron microscopes,provide,"much higher magnification, 100,000x","a) Most light microscopes in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers. b) Electron microscopes provide a much higher magnification, 100,000x, and a have a resolution of 50 picometers."
-electron microscopes,have a resolution of,50 picometers,"a) Most light microscopes in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers. b) Electron microscopes provide a much higher magnification, 100,000x, and a have a resolution of 50 picometers."
-beam of electrons,allows for,higher magnification,"use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 4.3), it also provides higher resolving power."
-beam of electrons,allows for,more detail,"use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 4.3), it also provides higher resolving power."
-figure 4.3,demonstrates,use of a beam of electrons,"use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 4.3), it also provides higher resolving power."
-beam of electrons,provides,higher resolving power,"use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 4.3), it also provides higher resolving power."
-method,kills,specimen,"The method to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope."
-electrons,have,short wavelengths,"The method to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope."
-wavelengths,move best in,vacuum,"The method to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope."
-electron microscope,view,cells,"The method to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope."
-scanning electron microscope,moves back and forth across,cell's surface,"In a scanning electron microscope, a beam of electrons moves back and forth across a cell's surface, creating details of cell surface characteristics. In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell's internal structures."
-scanning electron microscope,creates details of,cell surface characteristics,"In a scanning electron microscope, a beam of electrons moves back and forth across a cell's surface, creating details of cell surface characteristics. In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell's internal structures."
-transmission electron microscope,penetrates,cell,"In a scanning electron microscope, a beam of electrons moves back and forth across a cell's surface, creating details of cell surface characteristics. In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell's internal structures."
-transmission electron microscope,provides details of,cell's internal structures,"In a scanning electron microscope, a beam of electrons moves back and forth across a cell's surface, creating details of cell surface characteristics. In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell's internal structures."
-electron microscopes,are,significantly more bulky and expensive than light microscopes,"As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes. a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope."
-salmonella bacteria,appear as,tiny purple dots when viewed with a light microscope,"As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes. a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope."
-salmonella bacteria,can invade,human cells,"b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail."
-scanning electron microscope micrograph,shows,salmonella bacteria in red and human cells in yellow,"b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail."
-subfigure (b),shows,different salmonella specimen than subfigure (a),"b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail."
-microscopes,are,complex,"For another perspective on cell size, try the HowBig interactive at this site. The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s."
-microscopes,used today,more complex than those,"For another perspective on cell size, try the HowBig interactive at this site. The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s."
-antony van leeuwenhoek,used,microscopes in the 1600s,"For another perspective on cell size, try the HowBig interactive at this site. The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s."
-van leeuwenhoek,was skilled in,crafting lenses,"Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-van leeuwenhoek,observed,movements of single-celled organisms,"Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-van leeuwenhoek,termed,"single-celled organisms ""animalcules""","Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-robert hooke,coined,"term ""cell""","Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-robert hooke,observed,box-like structures when viewing cork tissue through a lens,"Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed ""animalcules."" In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term ""cell"" for the box-like structures he observed when viewing cork tissue through a lens."
-van leeuwenhoek,discovered,bacteria,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells."
-van leeuwenhoek,discovered,protozoa,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells."
-advances,enabled,scientists,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells."
-lenses,enabled,scientists,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells."
-microscope construction,enabled,scientists,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells."
-staining techniques,enabled,scientists,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells."
-scientists,see,components,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells."
-components,inside,cells,"In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells."
-matthias schleiden,were studying,tissues,"By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory."
-theodor schwann,were studying,tissues,"By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory."
-matthias schleiden and theodor schwann,proposed,unified cell theory,"By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory."
-unified cell theory,states that,one or more cells comprise all living things,"By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory."
-unified cell theory,states that,cell is the basic unit of life,"By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory."
-unified cell theory,states that,new cells arise from existing cells,"By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory."
-rudolf virchow,made,important contributions to the unified cell theory,"By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory."
-pap smear,involves,taking a small sample of cells,"Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-pap smear,is,medical test,"Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-cells,taken from,patient's uterine cervix,"Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-sample,sent to,medical lab,"Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-cytotechnologist,stains,cells,"Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-cytotechnologist,examines,cells for any changes,"Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-changes,could indicate,cervical cancer,"Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-changes,could indicate,microbial infection,"Have you ever heard of a medical test called a Pap smear (Figure 4.4)? In this test, a doctor takes a small sample of cells from the patient's uterine cervix and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection."
-cytotechnologists,study,cells,"Cytotechnologists (cyto- = ""cell"") are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal."
-cytotechnologists,are,professionals,"Cytotechnologists (cyto- = ""cell"") are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal."
-cytotechnologists,trained to determine,which cellular changes are within normal limits,"Cytotechnologists (cyto- = ""cell"") are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal."
-cytotechnologists,trained to determine,which cellular changes are abnormal,"Cytotechnologists (cyto- = ""cell"") are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal."
-study,has focus on,cervical cells,Their focus is not limited to cervical cells. They study cellular specimens that come from all organs.
-study,has focus on,cellular specimens,Their focus is not limited to cervical cells. They study cellular specimens that come from all organs.
-cellular specimens,come from,all organs,Their focus is not limited to cervical cells. They study cellular specimens that come from all organs.
-abnormalities,noticed by,people,"When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-people,consult,pathologist,"When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-pathologist,is,medical doctor,"When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-medical doctor,interprets and diagnoses,changes,"When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-changes,caused by,disease,"When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-disease,in body tissue and fluids,cause,"When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-cytotechnologists,play,vital role,"When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-vital role,in saving,people's lives,"When they notice abnormalities, they consult a pathologist, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause. Cytotechnologists play a vital role in saving people's lives."
-doctors,discover,abnormalities,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear."
-abnormalities,can begin,treatment,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear."
-treatment,increases chances of,successful outcome,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear."
-uterine cervix cells,viewed through,light microscope,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear."
-uterine cervix cells,from,pap smear,"When doctors discover abnormalities early, a patient's treatment can begin sooner, which usually increases the chances of a successful outcome. These uterine cervix cells, viewed through a light microscope, are from a Pap smear."
-normal cells,on,left,Normal cells are on the left. The cells on the right are infected with human papillomavirus (HPV).
-cells on the right,infected with,human papillomavirus (hpv),Normal cells are on the left. The cells on the right are infected with human papillomavirus (HPV).
-infected cells,are,larger,"Notice that the infected cells are larger. Also, two of these cells each have two nuclei instead of one, the normal number."
-cells,have,nuclei,"Notice that the infected cells are larger. Also, two of these cells each have two nuclei instead of one, the normal number."
-cells,have,two nuclei,"Notice that the infected cells are larger. Also, two of these cells each have two nuclei instead of one, the normal number."
-cells,have,one nuclei,"Notice that the infected cells are larger. Also, two of these cells each have two nuclei instead of one, the normal number."
-cells,have,normal number,"Notice that the infected cells are larger. Also, two of these cells each have two nuclei instead of one, the normal number."

process.py → utils.py

@@ -5,6 +5,7 @@ import re
 stop_words = stopwords.words("english")
 
 def process(df: DataFrame):
+    """Text2KG post-processing."""
     drop_list = []
 
     for i, row in df.iterrows():

visualize.py

@@ -1,26 +0,0 @@
-import networkx as nx
-import matplotlib.pyplot as plt
-import pandas as pd
-
-
-def visualize(data: pd.DataFrame):
-    G = nx.from_pandas_edgelist(
-        data,
-        source="subject",
-        target="object",
-        edge_attr="relation",
-        edge_key="relation",
-        create_using=nx.MultiDiGraph()
-    )
-
-    plt.ion()
-    plt.figure(figsize=(32, 32))
-    nx.draw_networkx(G, 
-                     with_labels=True, 
-                     pos=nx.spring_layout(G))
-    # nx.draw_networkx_edge_labels(G,
-    #                              edge_labels=...,
-    #                              pos=nx.spring_layout(G))
-    plt.show()
-
-