Difference between revisions of "Ontology meeting 2020-01-13"

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* Should we capture alternative ways to form URLs ? Or just a single recommended URL ? For example Jen Smith from RGD wrote:  
 
* Should we capture alternative ways to form URLs ? Or just a single recommended URL ? For example Jen Smith from RGD wrote:  
 
"that URL will work even if the prefix ("RGD:") is included with the ID (e.g., https://rgd.mcw.edu/rgdweb/search/search.html?term=RGD:2004).  In case it's helpful for you to know that."
 
"that URL will work even if the prefix ("RGD:") is included with the ID (e.g., https://rgd.mcw.edu/rgdweb/search/search.html?term=RGD:2004).  In case it's helpful for you to know that."
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===Relations===
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* preceded_by/precedes: https://github.com/geneontology/go-ontology/issues/18515
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* coincident_with: 6 terms in the ontology, about 300 annotations:
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** Example term: chromosome, centromeric core domain -
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**Example annotations:
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*** sep1 forkhead transcription factor Sep1 '''nuclear chromatin''' '''coincident with SO:0001871 (PCB - promoter element)''' PomBase Schizosaccharomyces pombe IDA forkhead box protein pthr11829 protein PMID:25908789 20150828
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*** -> should be occurs_at (now replaced by occurs_in? )
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*** sep1 forkhead transcription factor Sep1 '''nuclear chromatin''' '''coincident with PomBase:SPAC1705.03c''' PomBase Schizosaccharomyces pombe IDA forkhead box protein pthr11829 protein PMID:25908789
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*** -> should not be annotated ?
  
 
==Other Business==
 
==Other Business==

Latest revision as of 09:59, 13 January 2020

Conference Line

See calendar for details

On call:

Agenda

Discussion topics

Guidelines for definition cross references

(Pascale): There are several tickets, including #16895 and #18288 where guidelines are requested to define what is allowed in definition cross references.


In ticket #16895 David writes "I would like to see the definition xrefs reserved for stable publications that support the existence, placement and definition of a term."

  • Should we make this the guideline ?
  • How about " [GOC:initials], [GOC:goc_curators] and [GOC:curators]? We have loads of those.
  • How about EC and Rhea ?
  • How about InterPro and Pfam ?
  • How about wikipedia ?

Updating dbxref file

(Pascale): Cleaned and removed several stale dbxref (ie when links are not working: https://github.com/geneontology/go-site/issues/1263). Updated several xrefs, for example https://github.com/geneontology/go-site/issues/1293

Questions:

  • What is the purpose of this file ? The .md file [1] states "This is the source file for the GO prefix registry."; so if we are not using the prefix presumably we don' need it ?
  • When I deleted a db I checked that it wasn't cited in the ontology file and that the namespace was not in the 'Contributors' in AmiGO.
  • Some resources have various amounts of information, it would be nice to know the appropriate amount of information needed

For example with Harold we are not sure 'MGI Variant' is needed, since the link to any MGI object is constructed the same way. Why capture that, and not MGI allele, strain, reference, etc ?

  • Should we capture alternative ways to form URLs ? Or just a single recommended URL ? For example Jen Smith from RGD wrote:

"that URL will work even if the prefix ("RGD:") is included with the ID (e.g., https://rgd.mcw.edu/rgdweb/search/search.html?term=RGD:2004). In case it's helpful for you to know that."

Relations

  • preceded_by/precedes: https://github.com/geneontology/go-ontology/issues/18515
  • coincident_with: 6 terms in the ontology, about 300 annotations:
    • Example term: chromosome, centromeric core domain -
    • Example annotations:
      • sep1 forkhead transcription factor Sep1 nuclear chromatin coincident with SO:0001871 (PCB - promoter element) PomBase Schizosaccharomyces pombe IDA forkhead box protein pthr11829 protein PMID:25908789 20150828
      • -> should be occurs_at (now replaced by occurs_in? )
      • sep1 forkhead transcription factor Sep1 nuclear chromatin coincident with PomBase:SPAC1705.03c PomBase Schizosaccharomyces pombe IDA forkhead box protein pthr11829 protein PMID:25908789
      • -> should not be annotated ?

Other Business

https://github.com/geneontology/go-ontology/projects/1

Minutes should be recorded on individual tickets and in individual projects