Ontology meeting 2014-03-13
Attendees: Paola, DavidOS, DavidH, Chris, Heiko, Tanya, Harold
New release of OBO-Edit
Release 2.3.1-b1 is available for testing (https://sourceforge.net/projects/geneontology/)
The only change is support for annotation properties (e.g. neverintaxon).
Everyone will need to switch to 2.3.1 before moving taxon constraints (TCs) into editors' file: https://www.ebi.ac.uk/panda/jira/browse/GO-267#comment-92325
We need to do some more testing of 2.3.1b first, but we don't anticipate any issues.
Where are we with this?
Editors to download and test. Pls. do ASAP. Release will be done right after meeting.
'colocalizes with' nuclear chromatin
Experiment: gene product is bound to nuclear chromatin, specifically the pol3 promoter of gene X
Proposed changes: need new GO cell component term , chromosomal region/segment (domain), pol3 promoter (SO term), new relationship 'coincident with', of Annotation: Genus/col5: GO:new ! chromosome segment, col16: col16: coincident_with(SO:nnnn)! pol3 prom, part_of(GO:0000790)! nuclear chromatin, coincident_with gene_product_id (MGI:MGI:nnnnnn)
Ontology edits: need to change complex terms that are is_a children of nuclear chromatin to be part_of - open JIRA issue
New relationship type: add 'coincident with' to RO with generic definition - DavidOS to add to RO
Related problem: cytoskeleton child terms that are is_a and should probably be part_of - open JIRA issue
Carried over from annotation call on Tuesday. Create new component terms. Discuss.
http://gocwiki.geneontology.org/index.php/Annotation_Conf._Call,_March_11,_2014#Curation_question My point was that adding a new relation doesn't help as you're still making a statement SUBUNITX colocalizeswith some (nuclearchromatin AND some pol3promoter) The subunit needs to be connected directly with the promoter to ensure the interpretation is as strong as intended. I recommended adding new terms to the ontology that are parts of chromatin that are cognates of the SO sequences. I also suggested that =has_part would be logically valid but weaker than the intent. However, I then realized I wasn't completely sure on the strict meaning of nuclear chromatin in GO - does it mean the entirety or a portion? This is one of those situations where it's actually important to be clear. I found the highlighted placements a little odd: is_a GO:0044428 ! nuclear part is_a GO:0044454 ! nuclear chromosome part is_a GO:0000790 ! nuclear chromatin is_a GO:0005719 ! nuclear euchromatin is_a GO:0005720 ! nuclear heterochromatin is_a GO:0001739 ! sex chromatin is_a GO:0005724 ! nuclear telomeric heterochromatin is_a GO:0005725 ! intercalary heterochromatin is_a GO:0031618 ! nuclear centromeric heterochromatin is_a GO:0098578 ! condensed chromatin of inactivated sex chromosome is_a GO:0098580 ! chromatin of active sex chromosome is_a GO:1902377 ! nuclear rDNA heterochromatin is_a GO:0070209 ! ASTRA complex* is_a GO:0070211 ! Snt2C complex* is_a GO:0070823 ! HDA1 complex* is_a GO:0098580 ! chromatin of active sex chromosome Maybe these are mistakes, and the intention is part_of? But it seems the intention is that NC can be any portion - which allows us to make a class expression with the intended meaning (nuclearchromatin and hasdnapartconsistingonlyof some RNAPol3_promoter) Not suggesting this actual relation, just to demonstrate the possibility. I think it's cleaner to flip around the class expression and make the promoter region the genus. Or alternatively, to make the genus (col5 in a GAF) some generic small chromosome region and include two part_of differentia, to NC and to the promoter. There's a wider issue here about the gap between the interpretation a reasoner might make and those a curator might make, especially if the curation tool doesn't make use of reasoning to test the generated expression. I can see how this might be frustrating for CC annotations where the intent is to make an expression that is part_of the GO CC class. Anyway, I said we would discuss on thursday.
see also - discussion in thread "Re: [go-discuss] annotation extensions: relation to use for localization to chromosome at specific sequence feature" from Jan/Feb 14
Brief discussion on presentations for GOC Saturday meeting and slides.