NCBO Wiki - User contributions [en]

SO:gene

2006-08-10T16:56:55Z

Eilbeck:

http://song.sourceforge.net/SO_view/term_tables.html#gene

The term gene was the hardest term in the ontology to define. We were not looking for your standard unit of inheritance definition, but needed something more concrete to be able to pin this term down to a location on sequence, and be able to reason over the parts of gene annotations. To define the term gene in SO, we asked several questions. What is the extent of a gene on biological sequence? What are its parts? Can it have parts that are geographically disjoint? What is the relationship between a gene and regulatory regions like enhancers and promoters. What is the product of a gene? Do we need to revise our understanding of the relationships we are using? Is the part_of relationship sufficient to describe the parts of a gene? What do we mean by part_of anyway?

We agreed that genes are associated with regulatory regions and transcripts. In the canonical gene annotation,[song.sourceforge.net/gff3.shtml] a transcript sequence can be located within the gene sequence and a gene is therefore composed of parts: transcripts, exons, introns, promotors etc. But this solution does not work for cases where the regulatory regions are dispersed to the point of being on different chromosomes, the gene is trans-spliced, or polycistronic. The problem was that we were making topological assumptions about the part_of relation.

This lead us to consider the part_of relationship we had been using to naively describe the structure of our gene. The implication being that if a region of sequence is a part_of another region of sequence, then the parts coordinates will be located within the wholes coordinates. This is not always true for some of the parts of a gene. Do we mean different things when we call something a part? There is much written about parts and mereology, which is out of the scope of the discussion of genes, but the part_of relationship can be divided into subtypes based on three criteria: substance, configuration and invariance. (Winston et al)

Relating this back to SO we found that we had two different kinds of part_of in the ontology: composite part_of object (exon composite_part_of transcript) and member part_of collection (regulatory_region member_part_of gene).

So a gene is thought of as a collection of transcripts and regulatory_regions. Transcripts on the other hand are composite objects made of exons and introns. It makes no sense for an intron to be located out of the bondary of a transcript. The type of gene: protein_coding, or non_protein _coding is captured by the kind of transcript it produces such as mRNA, tRNA etc.

The SO textual definition of gene:
''A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions.''

= References: =

SO meetings 2004 http://song.sourceforge.net/SO_meeting.shtml

Winston M, Chaffin R, Herrmann : A taxonomy of part-whole relations. Cog Sci 1987, 11:417-444.

Region

2006-08-10T16:40:39Z

Eilbeck:

= Rationale for the regions in SO =

[[SO:gene]]

SO term rationale

2006-08-09T19:57:38Z

Eilbeck:

== Welcome to the SO term rationale ==

This term rationale is provided to explain the reasoning of design decisions made when creating the Sequence Ontology.

The main division within the Sequence Ontology is between terms that describe an extent of sequence, called [[located_sequence_features]], and those terms that describe a quality of a feature, called [[sequence_attributes]]. There are several [[SO_relationships]] used in SO to relate the terms.

Located sequence features

2006-08-09T19:52:47Z

Eilbeck:

Located_sequence_feature are terms that represent an extent of sequence and can be described in terms of coordinates. There are 2 kinds of located_sequence_feature; [[region]]s whose extent is >= 1, and [[junction]]s where the exent is 0, implying the location between bases. This division was necessary to define terms that refer to a length of bases and those terms that refer only to the boundary between bases.

Located sequence features

2006-08-09T18:27:02Z

Eilbeck:

SO term rationale

2006-08-09T18:23:14Z

Eilbeck:

Sequence attributes

2006-08-09T18:22:32Z

Eilbeck:

'''Sequence_attributes''' are terms that describe a quality of a biological feature. These terms cannot be located on sequence by themselves, but must be paired with the feature that they describe. For example, '''engineered''' is an attribute, that can describe may kinds of feature such as plasmids, genes and transposable elements.

SO term rationale

2006-08-09T17:36:48Z

Eilbeck:

== Welcome to the SO term rationale ==

This term rationale is provided to explain the reasoning of design decisions made when creating the Sequence Ontology.

The main division within the Sequence Ontology is between terms that describe an extent of sequence, called [[locatable_sequence_features]], and those terms that describe a quality of a feature, called [[sequence_attributes]].

SO term rationale

2006-07-14T20:51:25Z

Eilbeck:

== Welcome to the SO term rationale ==

This is a work in progress...

SO:Main Page

2006-07-14T20:50:02Z

Eilbeck: /* Resources */

=SO - Sequence Ontology=

Welcome to the Sequence Ontology wiki.

=Resources=

==Ontology==

The Sequence Ontology is currently hosted at: http://song.sourceforge.net

The ontology terms can be browsed using miSO: http://song.sourceforge.net/SO_view/index.html

==Request tracker==

Term tracker: http://sourceforge.net/tracker/?group_id=72703&atid=810408

==Mail Lists==

The developers mailing list: http://sourceforge.net/mail/?group_id=72703

==Term rationale==

The [[SO term rationale]] is an on going endeavour to provide explanations of the terms in the ontology. This will include links to the mailing list discussion of the terms, and the minutes of meetings etc.

==FAQ==

SO FAQ: http://song.sourceforge.net/SOFAQ.shtml

=Events=

SO workshop for plasmids, phages, transposons and other mobile elements. The workshop will be held at the Wellcome Trust Convention Centre, Hinxton, on September 18-19th 2006. http://song.sourceforge.net/workshop.shtml

=Publications=
The Sequence Ontology: A tool for the unification of genome annotations. Eilbeck K., Lewis S.E., Mungall C.J., Yandell M., Stein L., Durbin R., Ashburner M Genome Biology (2005) 6:R44

Sequence Ontology Annotation Guide. Karen Eilbeck and Suzanna E. Lewis. Comparative and Functional Genomics (2004) 5:642-647

SO:Main Page

2006-07-14T20:40:29Z

Eilbeck: /* Resources */

=SO - Sequence Ontology=

Welcome to the Sequence Ontology wiki.

=Resources=

==Ontology==

The Sequence Ontology is currently hosted at: http://song.sourceforge.net

The ontology terms can be browsed using miSO: http://song.sourceforge.net/SO_view/index.html

==Request tracker==

Term tracker: http://sourceforge.net/tracker/?group_id=72703&atid=810408

==Mail Lists==

The developers mailing list: http://sourceforge.net/mail/?group_id=72703

=Events=

SO workshop for plasmids, phages, transposons and other mobile elements. The workshop will be held at the Wellcome Trust Convention Centre, Hinxton, on September 18-19th 2006. http://song.sourceforge.net/workshop.shtml

=Publications=
The Sequence Ontology: A tool for the unification of genome annotations. Eilbeck K., Lewis S.E., Mungall C.J., Yandell M., Stein L., Durbin R., Ashburner M Genome Biology (2005) 6:R44

Sequence Ontology Annotation Guide. Karen Eilbeck and Suzanna E. Lewis. Comparative and Functional Genomics (2004) 5:642-647

SO:Main Page

2006-07-14T20:00:43Z

Eilbeck: /* SO - Sequence Ontology */

=SO - Sequence Ontology=

Welcome to the Sequence Ontology wiki.

=Resources=

==Ontology==

The Sequence Ontology is currently hosted at: http://song.sourceforge.net

==Request tracker==

Term tracker: http://sourceforge.net/tracker/?group_id=72703&atid=810408

==Mail Lists==

The developers mailing list: http://sourceforge.net/mail/?group_id=72703

=Events=

SO workshop for plasmids, phages, transposons and other mobile elements. The workshop will be held at the Wellcome Trust Convention Centre, Hinxton, on September 18-19th 2006. http://song.sourceforge.net/workshop.shtml

=Publications=
The Sequence Ontology: A tool for the unification of genome annotations. Eilbeck K., Lewis S.E., Mungall C.J., Yandell M., Stein L., Durbin R., Ashburner M Genome Biology (2005) 6:R44

Sequence Ontology Annotation Guide. Karen Eilbeck and Suzanna E. Lewis. Comparative and Functional Genomics (2004) 5:642-647

SO:Main Page

2006-07-14T19:59:11Z

Eilbeck:

=SO - Sequence Ontology=

=Resources=

==Ontology==

The Sequence Ontology is currently hosted at: http://song.sourceforge.net

==Request tracker==

Term tracker: http://sourceforge.net/tracker/?group_id=72703&atid=810408

==Mail Lists==

The developers mailing list: http://sourceforge.net/mail/?group_id=72703

=Events=

SO workshop for plasmids, phages, transposons and other mobile elements. The workshop will be held at the Wellcome Trust Convention Centre, Hinxton, on September 18-19th 2006. http://song.sourceforge.net/workshop.shtml

=Publications=
The Sequence Ontology: A tool for the unification of genome annotations. Eilbeck K., Lewis S.E., Mungall C.J., Yandell M., Stein L., Durbin R., Ashburner M Genome Biology (2005) 6:R44

Sequence Ontology Annotation Guide. Karen Eilbeck and Suzanna E. Lewis. Comparative and Functional Genomics (2004) 5:642-647

Main Page

2006-07-14T19:39:44Z

Eilbeck: /* Ontology Development Area */

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, 
dissemination events conducted by the NCBO and publically shared materials from the NCBO.

=== NCBO Links ===
*[http://www.bioontology.org/ NCBO Home page]
*[http://www.bioontology.org/wiki/index.php/CBio_FAQ NCBO FAQ]
*[[Meetings and Events]]

=== Shared Materials===

*[[Shared Materials]]

*[[Evaluation Activities]]

=== Other NCBC Links ===

*[http://www.bisti.nih.gov/ncbc/ NCBC Home page]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]

=== Ontology Development Area ===

Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki

*[[PATO:Main_Page]] - An ontology of phenotypic qualities

*[[RO:Main_Page]] - OBO Relations ontology

*[[CARO:Main_Page]] - Reference anatomical ontology

*[[CL:Main_Page]] - OBO Cell ontology

*[[SO:Main_Page]] - Sequence Ontology

Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.