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| <!-- ============================================ | |
| ::DATATOOL:: Generated from "insdseq.asn" | |
| ::DATATOOL:: by application DATATOOL version 2.0.0 | |
| ::DATATOOL:: on 08/02/2010 23:05:14 | |
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| <!-- ============================================ --> | |
| <!-- This section is mapped from module "INSD-INSDSeq" | |
| ================================================= --> | |
| <!-- | |
| $Revision: 192674 $ | |
| ************************************************************************ | |
| ASN.1 and XML for the components of a GenBank/EMBL/DDBJ sequence record | |
| The International Nucleotide Sequence Database (INSD) collaboration | |
| Version 1.6, 25 May 2010 | |
| ************************************************************************ | |
| --> | |
| <!-- | |
| INSDSeq provides the elements of a sequence as presented in the | |
| GenBank/EMBL/DDBJ-style flatfile formats, with a small amount of | |
| additional structure. | |
| Although this single perspective of the three flatfile formats | |
| provides a useful simplification, it hides to some extent the | |
| details of the actual data underlying those formats. Nevertheless, | |
| the XML version of INSD-Seq is being provided with | |
| the hopes that it will prove useful to those who bulk-process | |
| sequence data at the flatfile-format level of detail. Further | |
| documentation regarding the content and conventions of those formats | |
| can be found at: | |
| URLs for the DDBJ, EMBL, and GenBank Feature Table Document: | |
| http://www.ddbj.nig.ac.jp/FT/full_index.html | |
| http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html | |
| http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html | |
| URLs for DDBJ, EMBL, and GenBank Release Notes : | |
| ftp://ftp.ddbj.nig.ac.jp/database/ddbj/ddbjrel.txt | |
| http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.html | |
| ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt | |
| Because INSDSeq is a compromise, a number of pragmatic decisions have | |
| been made: | |
| In pursuit of simplicity and familiarity a number of fields do not | |
| have full substructure defined here where there is already a | |
| standard flatfile format string. For example: | |
| Dates: DD-MON-YYYY (eg 10-JUN-2003) | |
| Author: LastName, Initials (eg Smith, J.N.) | |
| or Lastname Initials (eg Smith J.N.) | |
| Journal: JournalName Volume (issue), page-range (year) | |
| or JournalName Volume(issue):page-range(year) | |
| eg Appl. Environ. Microbiol. 61 (4), 1646-1648 (1995) | |
| Appl. Environ. Microbiol. 61(4):1646-1648(1995). | |
| FeatureLocations are representated as in the flatfile feature table, | |
| but FeatureIntervals may also be provided as a convenience | |
| FeatureQualifiers are represented as in the flatfile feature table. | |
| Primary has a string that represents a table to construct | |
| a third party (TPA) sequence. | |
| other-seqids can have strings with the "vertical bar format" sequence | |
| identifiers used in BLAST for example, when they are non-INSD types. | |
| Currently in flatfile format you only see Accession numbers, but there | |
| are others, like patents, submitter clone names, etc which will | |
| appear here | |
| There are also a number of elements that could have been more exactly | |
| specified, but in the interest of simplicity have been simply left as | |
| optional. For example: | |
| All publicly accessible sequence records in INSDSeq format will | |
| include accession and accession.version. However, these elements are | |
| optional in optional in INSDSeq so that this format can also be used | |
| for non-public sequence data, prior to the assignment of accessions and | |
| version numbers. In such cases, records will have only "other-seqids". | |
| sequences will normally all have "sequence" filled in. But contig records | |
| will have a "join" statement in the "contig" slot, and no "sequence". | |
| We also may consider a retrieval option with no sequence of any kind | |
| and no feature table to quickly check minimal values. | |
| Four (optional) elements are specific to records represented via the EMBL | |
| sequence database: INSDSeq_update-release, INSDSeq_create-release, | |
| INSDSeq_entry-version, and INSDSeq_database-reference. | |
| One (optional) element is specific to records originating at the GenBank | |
| and DDBJ sequence databases: INSDSeq_segment. | |
| ******** | |
| --> | |
| <!-- Optional for contig, wgs, etc. --> | |
| <!-- | |
| INSDReference_position contains a string value indicating the | |
| basepair span(s) to which a reference applies. The allowable | |
| formats are: | |
| X..Y : Where X and Y are integers separated by two periods, | |
| X >= 1 , Y <= sequence length, and X <= Y | |
| Multiple basepair spans can exist, separated by a | |
| semi-colon and a space. For example : 10..20; 100..500 | |
| sites : The string literal 'sites', indicating that a reference | |
| provides sequence annotation information, but the specific | |
| basepair spans are either not captured, or were too numerous | |
| to record. | |
| The 'sites' literal string is singly occuring, and | |
| cannot be used in conjunction with any X..Y basepair spans. | |
| References that lack an INSDReference_position element apply | |
| to the entire sequence. | |
| --> | |
| <!-- | |
| INSDXref provides a method for referring to records in | |
| other databases. INSDXref_dbname is a string value that | |
| provides the name of the database, and INSDXref_dbname | |
| is a string value that provides the record's identifier | |
| in that database. | |
| --> | |
| <!-- | |
| INSDFeature_operator contains a string value describing | |
| the relationship among a set of INSDInterval within | |
| INSDFeature_intervals. The allowable formats are: | |
| join : The string literal 'join' indicates that the | |
| INSDInterval intervals are biologically joined | |
| together into a contiguous molecule. | |
| order : The string literal 'order' indicates that the | |
| INSDInterval intervals are in the presented | |
| order, but they are not necessarily contiguous. | |
| Either 'join' or 'order' is required if INSDFeature_intervals | |
| is comprised of more than one INSDInterval . | |
| --> | |
| <!-- | |
| INSDInterval_iscomp is a boolean indicating whether | |
| an INSDInterval_from / INSDInterval_to location | |
| represents a location on the complement strand. | |
| When INSDInterval_iscomp is TRUE, it essentially | |
| confirms that a 'from' value which is greater than | |
| a 'to' value is intentional, because the location | |
| is on the opposite strand of the presented sequence. | |
| INSDInterval_interbp is a boolean indicating whether | |
| a feature (such as a restriction site) is located | |
| between two adjacent basepairs. When INSDInterval_iscomp | |
| is TRUE, the 'from' and 'to' values must differ by | |
| exactly one base. | |
| --> | |
| <!-- | |
| e.g., CON-division-join, WGS-contig-range, | |
| WGS-scaffold-range, MGA/CAGE-range, genome | |
| --> | |
| <!-- | |
| INSDInterval_iscomp is a boolean indicating whether | |
| an INSDInterval_from / INSDInterval_to location | |
| represents a location on the complement strand. | |
| When INSDInterval_iscomp is TRUE, it essentially | |
| confirms that a 'from' value which is greater than | |
| a 'to' value is intentional, because the location | |
| is on the opposite strand of the presented sequence. | |
| INSDInterval_interbp is a boolean indicating whether | |
| a feature (such as a restriction site) is located | |
| between two adjacent basepairs. When INSDInterval_iscomp | |
| is TRUE, the 'from' and 'to' values must differ by | |
| exactly one base. | |
| --> | |