Ontology meeting 2012-11-01

From GO Wiki
Jump to: navigation, search

MINUTES: David

ATTENDEES:David, Harold, Tanya, Paola, Jane, Heiko, Chris


Monthly update: Project Management in JIRA

See http://wiki.geneontology.org/index.php/Ontology_meeting_2012-09-12#Project_Management_in_JIRA



FOLLOW-UP: ChEBI paper

Judy has made comments on the paper, suggesting we split results and methods up more. If we did this we'd need more interesting results! Discuss with David and Tanya present.

Judy suggests that there should be less detailed text and more figures that maybe give one example in a figure. Tanya will go for the next round.


FOLLOW-UP: import/export template

Chris has a file. Ions mapped to atoms, need fixing. The Action Item from last week was for David and Tanya to do a second pass. Did they have a chance to look into this, or shall we move it to next week?

David and Tanya did not look at this in detail. They will do this by next week.


FOLLOW-UP: non-ChEBI parents for chemical terms

Discussed on email thread (subject: [go-ontology] CHEBI roles used in GO terms), but not fully resolved on yet. Last check with David and Tanya.

No more progress on this.


FOLLOW-UP: TermGenie template for non-template-able terms

Where are we on this?

The back end is almost ready. He is starting to work on the interface. Are there terms that we don't want created? Look through the obsolete list in GO. TG will check this. One concern is the gene-product specific terms.


TermGenie template for 'cellular response to'

This type of term is frequently requested via SF. I think we've discussed its addition previously, but don't remember if we reached a resolution - can't find anything on wiki or email threads. Would it be possible to implement a sort of 'decision tree' for the non-ChEBI parents? Or shall we leave this for the non-template-able term requests procedure?

E.g. see this SF request: https://sourceforge.net/tracker/?func=detail&aid=3580560&group_id=36855&atid=440764 [Paola]


The latest announcement (dated Sept. 12th) was for:

response to (a chemical compound)

(chemical compound) transmembrane transporter activity

part of cellular component

We haven't announced the 'chemical transmembrane transport' and 'chemical transporter activity' templates yet, have we? We've added GO:1901475 pyruvate transmembrane transport and GO:1901505 carbohydrate derivative transporter activity, so I assume these templates are safe to advertise. In fact, Antonia just used the 'uptake transmembrane transporter activity' one - https://sourceforge.net/tracker/?func=detail&aid=3580587&group_id=36855&atid=440764

Paola will send an e-mail. DONE.

The SF corner

GO:0010609 posttranscriptional regulation of gene expression by mRNA localization

See https://sourceforge.net/tracker/index.php?func=detail&aid=3580617&group_id=36855&atid=440764

Change to 'mRNA localization resulting in posttranscriptional regulation of gene expression' Paola will change. DONE.

Transport and localization logical definitions

From the latest email by Chris on this subject:

These are the asserted links we still can't re-infer. Mostly to do with targeting

EXISTS, NOT-ENTAILED SubClassOf(GO:0030150 'protein import into mitochondrial matrix' GO:0006626 'protein targeting to mitochondrion')

EXISTS, NOT-ENTAILED SubClassOf(GO:0032974 'amino acid export from vacuole' GO:0034487 'vacuolar amino acid transmembrane transport')

EXISTS, NOT-ENTAILED SubClassOf(GO:0032975 'amino acid import into vacuole' GO:0034487 'vacuolar amino acid transmembrane transport')

EXISTS, NOT-ENTAILED SubClassOf(GO:0045037 'protein import into chloroplast stroma' GO:0045036 'protein targeting to chloroplast')

EXISTS, NOT-ENTAILED SubClassOf(GO:0045038 'protein import into chloroplast thylakoid membrane' GO:0006612 'protein targeting to membrane')

EXISTS, NOT-ENTAILED SubClassOf(GO:0045038 'protein import into chloroplast thylakoid membrane' GO:0045036 'protein targeting to chloroplast')

EXISTS, NOT-ENTAILED SubClassOf(GO:0045039 'protein import into mitochondrial inner membrane' GO:0006612 'protein targeting to membrane')

EXISTS, NOT-ENTAILED SubClassOf(GO:0045039 'protein import into mitochondrial inner membrane' GO:0006626 'protein targeting to mitochondrion')

EXISTS, NOT-ENTAILED SubClassOf(GO:0045040 'protein import into mitochondrial outer membrane' GO:0006612 'protein targeting to membrane')

EXISTS, NOT-ENTAILED SubClassOf(GO:0045040 'protein import into mitochondrial outer membrane' GO:0006626 'protein targeting to mitochondrion')

EXISTS, NOT-ENTAILED SubClassOf(GO:0045041 'protein import into mitochondrial intermembrane space' GO:0006626 'protein targeting to mitochondrion')

EXISTS, NOT-ENTAILED SubClassOf(GO:0045046 'protein import into peroxisome membrane' GO:0006612 'protein targeting to membrane')

EXISTS, NOT-ENTAILED SubClassOf(GO:0045046 'protein import into peroxisome membrane' GO:0006625 'protein targeting to peroxisome')

Need to look at these relationships again. Shouldn't import be a part of targeting? Jane will look at this list.


On a related note: GO:0016197 ! endosomal transport and its children need revisiting (see email thread 'endosomal transport').

Do we need to split this term, rename it? Tanya will look at existing annotations to see how we have used it. Whatever happens, we need to fix the logical definition.


Ontology documentation

Chris would like to discuss that.

How do we assign credit to people contributing to GO? In addition, we need to remember the rationale for our decisions.

Should we use a knowledge blog? Might want to consider publishing things there. There is also a system whereby articles are modeled in a supplemental ontology. You can then refer to those in another ontology as well. So would something like the apoptosis documentation go there? That might go to the blog. Unless it is internal to us, we should get it out there.