https://wiki.geneontology.org/api.php?action=feedcontributions&user=Jdeegan&feedformat=atomGO Wiki - User contributions [en]2024-03-29T06:51:16ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Part_4&diff=25046Taxon-GO Checks and Commentary - Part 42010-02-24T10:57:11Z<p>Jdeegan: </p>
<hr />
<div>==General points about viruses in GO==<br />
<br />
===Terms that are implicitly used for both cellular organisms and invading viruses===<br />
<br />
There are a lot of processes that look, on the face of it, as though they should be specific to cellular organisms, but then they turn out also to be carried out by viruses inside of the cellular organisms. This is an interesting point to note for ontology development. Should we be using the same terms for:<br />
<br />
a) the process that is normal for a cellular organism to carry out in its own cell.<br><br />
b) the same process carried out by a virus that has invaded a host cell.<br />
<br />
Examples include the descendents of the terms cellular component organisation and cellular component biogenesis, that do not have the word 'cellular' at the beginning. <br />
<br />
==='Cellular' terms in GO - the converse of the above situation===<br />
<br />
Since we introduced the term 'cellular process' we have also started to make terms called 'cellular x', for example in the example below we will make the term 'cellular methylation'. This creation of parallel 'cellular x' and 'x' terms enables the natural process as carried out by a cellular organism to be annotator to the 'cellular x' term, while the same process as carried out by an invading virus in the host cell can be annotated to the non-cellular 'x' term. Is this the correct way to proceed? It involved a sort of duplication of a number of terms, though it does allow us to clearly distinguish between the host and viral processes. <br />
<br />
===Summary===<br />
<br />
Do the descendents with no 'cellular' at the beginning of the name trump the 'cellular' ancestor or vice versa, and what do we do about it?<br />
<br />
==Methylation in Viruses==<br />
<br />
GO:0032259 "methylation" only_in NCBITaxon:131567 "cellular organisms" :: PDB 1L9K_A 1L9K_A<br />
GO:0032259 GOA:interpro IEA InterPro:IPR002877 P <br />
protein_structure NCBITaxon:11060 20090629 UniProtKB<br />
<br />
There are virus annotations to methylation, but this is a type of cellular process. I have asked Jane and she says I need to make this the cellular methylation term and have a generic methylation term that is just under metabolic process and not under cellular process. <br />
<br />
[[Image:methylationInViruses.jpg]]</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24941Signaling to do list2010-02-16T17:39:57Z<p>Jdeegan: </p>
<hr />
<div><br />
==After merge and commit==<br />
<br />
Recheck intracellular signaling cascade. Somehow we had merged this into auxin signaling. I have unmerged before committing, but it would be good to take another look to see that I did the right thing. Perhaps it was meant to be merged into something else and landed in the wrong place in OBO-Edit?<br />
<br />
Fixed the created by and creation date tags on the signaling terms. The others are fine as I did those by hand. <br />
<br />
<br />
==Logical definitions==<br />
<br />
Project from Chris Mungall:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from <br />
one location to another. The process terminates at the end of the <br />
sub-process of signal transduction, when the function of the cell <br />
has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process<br />
of signal transmission. This implies that signal transduction is <br />
part_of signal transmission. Yet 'signal transduction' is an is_a <br />
child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship<br />
as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow <br />
of time on the x axis, with the processes arranged according to the <br />
allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ).<br />
Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded <br />
by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. <br />
I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should <br />
really be initiated_by <br />
<br />
</pre><br />
<br />
==Chris's Reactome2GO analysis==<br />
<br />
3 cols of 3:<br />
<br />
Pathway/Process<br><br />
Initiating event<br><br />
Initial Event<br />
<br />
Each is split into 3 - reactome label, GO ID, GO label<br />
<br />
(Jen: I have checked this into cvs [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/xps/r2go-signaling.txt go/scratch/xps/r2go-signaling.txt])<br />
<br />
Here initial event is a reactome leaf node in P that has no preceding event in P. initiation event is the event preceding this one.<br />
<br />
I would expect that for any pathway that has the GO def "..generated as a consequence of a X receptor binding to..." to have something like "X receptor binding" (or something that entails this) as an initiating event and perhaps something like "X receptor activity" as the first event in the process. Is this too simplistic?<br />
<br />
<br />
<br />
==Cross-references to Reactome==<br />
<br />
Peter D'Eustachio is making a list of GO terms and Reactome terms that could be cross referenced. Once he has completed this he will pass the list along to be intergrated into the GO ontology file.<br />
<br />
==Glutamate pathway==<br />
<br />
Invite Anita Bandrowski to meet with the signaling working group to make new terms for the glutamate pathway and related areas. (abandrowski at ucsd.edu)<br />
<br />
==Documentation==<br />
<br />
Work with the signaling working group to try to produce the kind of docs that Chris is interested to see:<br />
<br />
[[image:signalingDocExample.pdf]]<br><br />
[[Image:signalingDocExample.jpg]]</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Part_7&diff=24918Taxon-GO Checks and Commentary - Part 72010-02-11T11:19:29Z<p>Jdeegan: </p>
<hr />
<div>==Comments from WormBase, Ranjana Kishore and Kimberly Van Auken==<br />
<br />
==Taxon inconsistent terms coming from electronic annotation through the InterPro2GO pipeline==<br />
<pre><br />
GO:0042601 endospore-forming forespore <br />
GO:0009772 photosynthetic electron transport in photosystem II <br />
GO:0019684 photosynthesis, light reaction <br />
GO:0030077 plasma membrane light-harvesting complex <br />
GO:0015979 photosynthesis <br />
GO:0015995 chlorophyll biosynthetic process<br />
GO:0008316 structural constituent of vitelline membrane <br />
GO:0016032 viral reproduction<br />
</pre> <br />
<br />
For the above terms, should we communicate with InterPro2GO curators, that these mappings do not work for all species, or do we have to block these on our end?<br />
<br />
==Taxon inconsistent terms used in our annotation== <br />
<pre><br />
GO:0001703 gastrulation with mouth forming first <br />
</pre><br />
<br />
It is generally agreed that C. elegans belongs to the Protostomia, so annotations to this term should remain. <br />
Kimberly feels that the term itself might need some work. <br />
<br />
'''Possible changes:'''<br />
<br />
With respect to possible changes in the gastrulation branch of the ontology, one possibility would be to remove the protostome (GO:0001703, gastulation with mouth forming first) and deuterostome (GO:0001702, mouth forming second) terms and just have the current children of those terms be children of the more general gastrulation term, removing the reference to mouth forming first or second in those children.<br />
<br />
There is evidence now that there are mechanistic similarities between gastrulation in worms, flies, and vertebrates, so perhaps it'd be more helpful to users to be able to find gastrulation annotations together, where applicable, rather than under specific protostome/deuterostome terms.<br />
<br />
'''A recent review that touches on this is:'''<br />
<br />
Dev Dyn. 2009 Apr;238(4):789-96<br />
<br />
Polarity and cell fate specification in the control of Caenorhabditis elegans gastrulation.<br />
<br />
Rohrschneider MR, Nance J.<br />
<br />
Developmental Genetics Program, Skirball Institute of Biomolecular Medicine and Helen and Martin Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, New York 10016, USA.<br />
<br />
Gastrulation is a time during development when cells destined to produce internal tissues and organs move from the surface of the embryo into the interior. It is critical that the cell movements of gastrulation be precisely controlled, and coordinated with cell specification, in order for the embryo to develop normally. Caenorhabditis elegans gastrulation is relatively simple, can be observed easily in the transparent embryo, and can be manipulated genetically to uncover important regulatory mechanisms. Many of these cellular and molecular mechanisms, including cell shape, cytoskeletal, and cell cycle changes, appear to be conserved from flies to vertebrates. Here we review gastrulation in C. elegans, with an emphasis on recent data linking contact-induced cell polarity, PAR proteins, and cell fate specification to gastrulation control. Copyright 2009 Wiley-Liss, Inc.<br />
<br />
PMID: 19253398 [PubMed - indexed for MEDLINE] <br />
<br />
<pre><br />
GO:0001542 ovulation from ovarian follicle<br />
</pre><br />
<br />
We agree that the assignment of this term is inappropriate for C.elegans. It has been removed in our manual annotation database and replaced with the term 'ovulation'. This change will be reflected in our next upload to the GO consortium.<br />
<br />
<br />
==Photosynthesis==<br />
<br />
I have written to ask about these flagged errors:<br />
<br />
<pre><br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea"<br />
:: WB WBGene00003154 mcm-2 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea"<br />
:: WB WBGene00003155 mcm-3 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" <br />
:: WB WBGene00003156 mcm-4 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" <br />
:: WB WBGene00003159 mcm-7 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" <br />
:: WB WBGene00004503 rpt-3 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" <br />
:: WB WBGene00004505 rpt-5 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea"<br />
:: WB WBGene00007352 cdc-48.1 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" <br />
:: WB WBGene00008053 cdc-48.2 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea"<br />
:: WB WBGene00010842 ymel-1 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" <br />
:: WB WBGene00003154 mcm-2 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" <br />
:: WB WBGene00003155 mcm-3 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" <br />
:: WB WBGene00003156 mcm-4 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa"<br />
:: WB WBGene00003159 mcm-7 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" <br />
:: WB WBGene00004503 rpt-3 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" <br />
:: WB WBGene00004505 rpt-5 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" <br />
:: WB WBGene00007352 cdc-48.1 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa"<br />
:: WB WBGene00008053 cdc-48.2 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa"<br />
:: WB WBGene00010842 ymel-1 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
</pre><br />
<br />
Ranjana wrote back to say that these should be sent on to Emily at GOA as it is the InterPro2GO mapping that needs modified.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Part_7&diff=24916Taxon-GO Checks and Commentary - Part 72010-02-10T14:34:01Z<p>Jdeegan: </p>
<hr />
<div>==Comments from WormBase, Ranjana Kishore and Kimberly Van Auken==<br />
<br />
==Taxon inconsistent terms coming from electronic annotation through the InterPro2GO pipeline==<br />
<pre><br />
GO:0042601 endospore-forming forespore <br />
GO:0009772 photosynthetic electron transport in photosystem II <br />
GO:0019684 photosynthesis, light reaction <br />
GO:0030077 plasma membrane light-harvesting complex <br />
GO:0015979 photosynthesis <br />
GO:0015995 chlorophyll biosynthetic process<br />
GO:0008316 structural constituent of vitelline membrane <br />
GO:0016032 viral reproduction<br />
</pre> <br />
<br />
For the above terms, should we communicate with InterPro2GO curators, that these mappings do not work for all species, or do we have to block these on our end?<br />
<br />
==Taxon inconsistent terms used in our annotation== <br />
<pre><br />
GO:0001703 gastrulation with mouth forming first <br />
</pre><br />
<br />
It is generally agreed that C. elegans belongs to the Protostomia, so annotations to this term should remain. <br />
Kimberly feels that the term itself might need some work. <br />
<br />
'''Possible changes:'''<br />
<br />
With respect to possible changes in the gastrulation branch of the ontology, one possibility would be to remove the protostome (GO:0001703, gastulation with mouth forming first) and deuterostome (GO:0001702, mouth forming second) terms and just have the current children of those terms be children of the more general gastrulation term, removing the reference to mouth forming first or second in those children.<br />
<br />
There is evidence now that there are mechanistic similarities between gastrulation in worms, flies, and vertebrates, so perhaps it'd be more helpful to users to be able to find gastrulation annotations together, where applicable, rather than under specific protostome/deuterostome terms.<br />
<br />
'''A recent review that touches on this is:'''<br />
<br />
Dev Dyn. 2009 Apr;238(4):789-96<br />
<br />
Polarity and cell fate specification in the control of Caenorhabditis elegans gastrulation.<br />
<br />
Rohrschneider MR, Nance J.<br />
<br />
Developmental Genetics Program, Skirball Institute of Biomolecular Medicine and Helen and Martin Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, New York 10016, USA.<br />
<br />
Gastrulation is a time during development when cells destined to produce internal tissues and organs move from the surface of the embryo into the interior. It is critical that the cell movements of gastrulation be precisely controlled, and coordinated with cell specification, in order for the embryo to develop normally. Caenorhabditis elegans gastrulation is relatively simple, can be observed easily in the transparent embryo, and can be manipulated genetically to uncover important regulatory mechanisms. Many of these cellular and molecular mechanisms, including cell shape, cytoskeletal, and cell cycle changes, appear to be conserved from flies to vertebrates. Here we review gastrulation in C. elegans, with an emphasis on recent data linking contact-induced cell polarity, PAR proteins, and cell fate specification to gastrulation control. Copyright 2009 Wiley-Liss, Inc.<br />
<br />
PMID: 19253398 [PubMed - indexed for MEDLINE] <br />
<br />
<pre><br />
GO:0001542 ovulation from ovarian follicle<br />
</pre><br />
<br />
We agree that the assignment of this term is inappropriate for C.elegans. It has been removed in our manual annotation database and replaced with the term 'ovulation'. This change will be reflected in our next upload to the GO consortium.<br />
<br />
<br />
==Photosynthesis==<br />
<br />
I have written to ask about these flagged errors:<br />
<br />
<pre><br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea"<br />
:: WB WBGene00003154 mcm-2 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea"<br />
:: WB WBGene00003155 mcm-3 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" <br />
:: WB WBGene00003156 mcm-4 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" <br />
:: WB WBGene00003159 mcm-7 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" <br />
:: WB WBGene00004503 rpt-3 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" <br />
:: WB WBGene00004505 rpt-5 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea"<br />
:: WB WBGene00007352 cdc-48.1 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea" <br />
:: WB WBGene00008053 cdc-48.2 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015979 "photosynthesis" only_in NCBITaxon_Union:0000021 "Viridiplantae or Bacteria or Euglenozoa or Archaea"<br />
:: WB WBGene00010842 ymel-1 GO:0015979 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" <br />
:: WB WBGene00003154 mcm-2 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" <br />
:: WB WBGene00003155 mcm-3 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" <br />
:: WB WBGene00003156 mcm-4 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa"<br />
:: WB WBGene00003159 mcm-7 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" <br />
:: WB WBGene00004503 rpt-3 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" <br />
:: WB WBGene00004505 rpt-5 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa" <br />
:: WB WBGene00007352 cdc-48.1 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa"<br />
:: WB WBGene00008053 cdc-48.2 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
GO:0015995 "chlorophyll biosynthetic process" only_in NCBITaxon_Union:0000007 "Viridiplantae or Bacteria or Euglenozoa"<br />
:: WB WBGene00010842 ymel-1 GO:0015995 PMID:12520011|PMID:12654719 IEA INTERPRO:IPR000523<br />
P gene NCBITaxon:6239 20091126 WB <br />
<br />
</pre></div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Part_11&diff=24915Taxon-GO Checks and Commentary - Part 112010-02-10T14:25:26Z<p>Jdeegan: </p>
<hr />
<div>Sent this mail to the appropriate groups. <br />
<br />
<br />
<pre><br />
Hi,<br />
<br />
I have just added a checking rule:<br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi"<br />
<br />
and a number of annotations have been flagged (listed below). Could you <br />
possibly have a look at the ones from your databases and let me know <br />
whether it's the annotation or the rule?<br />
<br />
Thanks,<br />
<br />
Jen<br />
<br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: MGI<br />
MGI:1923036 Ckap5 GO:0051300 MGI:MGI:2154458 ISO <br />
EMBL:X92474 P gene NCBITaxon:10090 20060111 MGI <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: RGD<br />
1307071 RGD1307071 GO:0051300 RGD:1624291 ISO <br />
RGD:1316045 P gene NCBITaxon:10116 20100129 RGD <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: RGD<br />
1566336 Cep72 GO:0051300 RGD:1624291 ISO <br />
RGD:1603993 P gene NCBITaxon:10116 20100129 RGD <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: RGD<br />
621258 Kif11 GO:0051300 RGD:1600115 IEA <br />
Ensembl:ENSP00000260731 P gene NCBITaxon:10116 20100119 <br />
ENSEMBL <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: RGD<br />
621258 Kif11 GO:0051300 RGD:1624291 ISO <br />
RGD:1346274 P gene NCBITaxon:10116 20100129 RGD <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
A0JNH1 KIZ GO:0051300 GO_REF:0000024 ISS UniProtKB:Q2M2Z5<br />
P protein NCBITaxon:9913 20090623 UniProtKB <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
A1L2H3 kiz GO:0051300 GO_REF:0000024 ISS UniProtKB:Q2M2Z5<br />
P protein NCBITaxon:8355 20090623 UniProtKB <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
P52732 KIF11 GO:0051300 PMID:14718566 IMP P<br />
protein NCBITaxon:9606 20060811 HGNC <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
Q14008 CKAP5 GO:0051300 PMID:14718566 IMP P<br />
protein NCBITaxon:9606 20060811 HGNC <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
Q2M2Z5 NCRNA00153 GO:0051300 PMID:16980960 IMP P<br />
protein NCBITaxon:9606 20090623 UniProtKB <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
Q5ZK13 KIZ GO:0051300 GO_REF:0000024 ISS UniProtKB:Q2M2Z5<br />
P protein NCBITaxon:9031 20090623 UniProtKB <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
Q9P209 CEP72 GO:0051300 PMID:19536135 IMP P <br />
protein NCBITaxon:9606 20090623 UniProtKB <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: TrEMBL<br />
Q5ZMS0 RCJMB04_1f15 GO:0051300 GO_REF:0000019 IEA <br />
Ensembl:ENSP00000260731 P protein NCBITaxon:9031 20100119 <br />
ENSEMBL <br />
</pre><br />
<br />
<br />
<br />
<br />
<br />
-- <br />
Jennifer Deegan (nee Clark)<br />
EMBL-European Bioinformatics Institute<br />
Gene Ontology Consortium</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Part_11&diff=24914Taxon-GO Checks and Commentary - Part 112010-02-10T14:25:04Z<p>Jdeegan: Created page with 'Sent this mail to the appropriate groups. <pre> Hi, I have just added a checking rule: GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" and a numb…'</p>
<hr />
<div>Sent this mail to the appropriate groups. <br />
<br />
<br />
<pre><br />
Hi,<br />
<br />
I have just added a checking rule:<br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi"<br />
<br />
and a number of annotations have been flagged (listed below). Could you <br />
possibly have a look at the ones from your databases and let me know <br />
whether it's the annotation or the rule?<br />
<br />
Thanks,<br />
<br />
Jen<br />
<br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: MGI<br />
MGI:1923036 Ckap5 GO:0051300 MGI:MGI:2154458 ISO <br />
EMBL:X92474 P gene NCBITaxon:10090 20060111 MGI <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: RGD<br />
1307071 RGD1307071 GO:0051300 RGD:1624291 ISO <br />
RGD:1316045 P gene NCBITaxon:10116 20100129 RGD <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: RGD<br />
1566336 Cep72 GO:0051300 RGD:1624291 ISO <br />
RGD:1603993 P gene NCBITaxon:10116 20100129 RGD <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: RGD<br />
621258 Kif11 GO:0051300 RGD:1600115 IEA <br />
Ensembl:ENSP00000260731 P gene NCBITaxon:10116 20100119 ENSEMBL <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: RGD<br />
621258 Kif11 GO:0051300 RGD:1624291 ISO <br />
RGD:1346274 P gene NCBITaxon:10116 20100129 RGD <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
A0JNH1 KIZ GO:0051300 GO_REF:0000024 ISS UniProtKB:Q2M2Z5<br />
P protein NCBITaxon:9913 20090623 UniProtKB <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
A1L2H3 kiz GO:0051300 GO_REF:0000024 ISS UniProtKB:Q2M2Z5<br />
P protein NCBITaxon:8355 20090623 UniProtKB <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
P52732 KIF11 GO:0051300 PMID:14718566 IMP P<br />
protein NCBITaxon:9606 20060811 HGNC <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
Q14008 CKAP5 GO:0051300 PMID:14718566 IMP P<br />
protein NCBITaxon:9606 20060811 HGNC <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
Q2M2Z5 NCRNA00153 GO:0051300 PMID:16980960 IMP P<br />
protein NCBITaxon:9606 20090623 UniProtKB <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
Q5ZK13 KIZ GO:0051300 GO_REF:0000024 ISS UniProtKB:Q2M2Z5<br />
P protein NCBITaxon:9031 20090623 UniProtKB <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot<br />
Q9P209 CEP72 GO:0051300 PMID:19536135 IMP P <br />
protein NCBITaxon:9606 20090623 UniProtKB <br />
<br />
GO:0051300 "spindle pole body organization" only_in NCBITaxon:4751 "Fungi" :: TrEMBL<br />
Q5ZMS0 RCJMB04_1f15 GO:0051300 GO_REF:0000019 IEA <br />
Ensembl:ENSP00000260731 P protein NCBITaxon:9031 20100119 ENSEMBL <br />
</pre><br />
<br />
<br />
<br />
<br />
<br />
-- <br />
Jennifer Deegan (nee Clark)<br />
EMBL-European Bioinformatics Institute<br />
Gene Ontology Consortium</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon_Main_Page&diff=24913Taxon Main Page2010-02-10T14:23:27Z<p>Jdeegan: </p>
<hr />
<div>[[Manuscript of taxon checking system paper]]<br />
<br />
[[Taxon Trigger File Metrics]]<br />
<br />
[[Proposal 2007]]<br />
<br />
[[Taxon-GO Implementation April 2008 onwards]]<br />
<br />
[[Taxon-GO Implementation April 2009 onwards]]<br />
<br />
[[Taxon-GO Checks and Commentary - Part 1]] - GOA and others<br />
<br />
[[Taxon-GO Checks and Commentary - Part 2]] - FlyBase<br />
<br />
[[Taxon-GO Checks and Commentary - Part 3]] - GOA<br />
<br />
[[Taxon-GO Checks and Commentary - Part 4]] - Viruses<br />
<br />
[[Taxon-GO Checks and Commentary - Part 5]] - MGI, ZFIN and SGD<br />
<br />
[[Taxon-GO Checks and Commentary - Part 6]] - TAIR, RGD and EcoCyc<br />
<br />
[[Taxon-GO Checks and Commentary - Part 7]] - WormBase<br />
<br />
[[Taxon-GO Checks and Commentary - Part 8]] - submission via SourceForge<br />
<br />
[[Taxon-GO Checks and Commentary - Response to GOA - Part 5]]<br />
<br />
[[Taxon-GO Checks and Commentary - Part 9]] - GOA<br />
<br />
[[Taxon-GO Checks and Commentary - Part 10]] - AgBase<br />
<br />
[[Taxon-GO Checks and Commentary - Part 11]] - Spindle pole body organization.<br />
<br />
[[Resolving redundancies in taxon links]]<br />
<br />
[[Taxon file location in cvs]]<br />
<br />
[[Union term id space]]<br />
<br />
[[To Do List - Taxon checks]]<br />
<br />
[[Are Multi-organism process and cellular process disjoint?]]<br />
<br />
<br />
[[Taxon Editing Workflow]] up until 12th June 2009<br />
<br />
[[Taxon Editing Workflow after 12th June 2009]]<br />
<br />
[[GAF_Taxonomy_Reasoning]]<br />
<br />
[[Category:Taxon]]</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Part_10&diff=24908Taxon-GO Checks and Commentary - Part 102010-02-10T13:01:25Z<p>Jdeegan: </p>
<hr />
<div>==New checks suggested by AgBase==<br />
<br />
Example line:<br />
<br />
GO:0007595 "lactation" only_in NCBITaxon:40674 "Mammalia" :: Ensembl ENSGALP00000029396 ENSGALP00000029396 GO:0007595 GO_REF:0000002 IEA InterPro:IPR003626 P protein NCBITaxon:9<br />
031 20091214 UniProtKB<br />
<br />
This IEA from Chicken is erroneously associates a protein with "lactation", which is restricted to mammals.<br />
<br />
Other examples that should only be applied to mammals are:<br />
<br />
<br />
GO:0001701 in utero embryonic development only_in Theria "taxon:32525"<br />
<br />
<br />
GO:0007595 lactation only_in Mammalia "taxon:40674"<br />
<br />
<br />
GO:0001890 placenta development only_in Theria "taxon:32525"<br />
<br />
<br />
GO:0030879 mammary gland development only_in Mammalia "taxon:40674"<br />
<br />
<br />
GO:0001967 suckling behaviour only_in Mammalia "taxon:40674"<br />
<br />
<br />
GO:0001824 blastocyst development only_in Theria "taxon:32525"<br />
<br />
'''NOTE:''' this classification needs checking; I am not sure if it is correct for marsupials.<br />
<br />
<br />
GO:0007565 female pregnancy only_in Mammalia "taxon:40674"<br />
<br />
<br />
GO:0042698 ovulation cycle only_in Mammalia "taxon:40674"<br />
<br />
<br />
GO:0042633 hair cycle only_in Mammalia "taxon:40674"<br />
<br />
GO:0042473 outer ear morphogenesis<br />
<br />
'''NOTE:''' chicken do not possess an outer ear, or pinna, as most mammals possess, but they do have ear lobes. Not sure whether this is included in the GO:0042473 definition<br />
<br />
GO:0042476 odontogenesis<br />
<br />
Exclude Aves "taxon:8782"<br />
<br />
Include Tyrannosauridae "taxon:436493" (eg. Tyrannosaurus rex - big scary teeth)<br />
<br />
<br />
GO:0042297 vocal learning only_in Passeriformes "taxon:9126"<br />
<br />
(Need to exclude all other Aves)<br />
<br />
'''DONE''': I have added all appropriate checks down to here.<br />
<br />
<br />
==Errors detected and fixed==<br />
<br />
The checks above produced 136 IEA errors which have been reported back for fixing.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Part_10&diff=24753Taxon-GO Checks and Commentary - Part 102010-02-05T11:11:06Z<p>Jdeegan: </p>
<hr />
<div>Example line:<br />
<br />
GO:0007595 "lactation" only_in NCBITaxon:40674 "Mammalia" :: Ensembl ENSGALP00000029396 ENSGALP00000029396 GO:0007595 GO_REF:0000002 IEA InterPro:IPR003626 P protein NCBITaxon:9<br />
031 20091214 UniProtKB<br />
<br />
This IEA from Chicken is erroneously associates a protein with "lactation", which is restricted to mammals.<br />
<br />
Other examples that should only be applied to mammals are:<br />
<br />
<br />
GO:0001701 in utero embryonic development only_in Theria "taxon:32525"<br />
<br />
<br />
GO:0007595 lactation only_in Mammalia "taxon:40674"<br />
<br />
<br />
GO:0001890 placenta development only_in Theria "taxon:32525"<br />
<br />
<br />
GO:0030879 mammary gland development only_in Mammalia "taxon:40674"<br />
<br />
<br />
GO:0001967 suckling behaviour only_in Mammalia "taxon:40674"<br />
<br />
<br />
GO:0001824 blastocyst development only_in Theria "taxon:32525"<br />
<br />
'''NOTE:''' this classification needs checking; I am not sure if it is correct for marsupials.<br />
<br />
<br />
GO:0007565 female pregnancy only_in Mammalia "taxon:40674"<br />
<br />
<br />
GO:0042698 ovulation cycle only_in Mammalia "taxon:40674"<br />
<br />
<br />
GO:0042633 hair cycle only_in Mammalia "taxon:40674"<br />
<br />
GO:0042473 outer ear morphogenesis<br />
<br />
'''NOTE:''' chicken do not possess an outer ear, or pinna, as most mammals possess, but they do have ear lobes. Not sure whether this is included in the GO:0042473 definition<br />
<br />
GO:0042476 odontogenesis<br />
<br />
Exclude Aves "taxon:8782"<br />
<br />
Include Tyrannosauridae "taxon:436493" (eg. Tyrannosaurus rex - big scary teeth)<br />
<br />
<br />
GO:0042297 vocal learning only_in Passeriformes "taxon:9126"<br />
<br />
(Need to exclude all other Aves)<br />
<br />
'''DONE''': I have added all appropriate checks down to here.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=File:SignalingDocExample.jpg&diff=24752File:SignalingDocExample.jpg2010-02-05T10:39:56Z<p>Jdeegan: uploaded a new version of "File:SignalingDocExample.jpg"</p>
<hr />
<div></div>Jdeeganhttps://wiki.geneontology.org/index.php?title=File:SignalingDocExample.jpg&diff=24751File:SignalingDocExample.jpg2010-02-05T10:39:47Z<p>Jdeegan: </p>
<hr />
<div></div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24750Signaling to do list2010-02-05T10:39:33Z<p>Jdeegan: </p>
<hr />
<div>==Logical definitions==<br />
<br />
Project from Chris Mungall:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from <br />
one location to another. The process terminates at the end of the <br />
sub-process of signal transduction, when the function of the cell <br />
has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process<br />
of signal transmission. This implies that signal transduction is <br />
part_of signal transmission. Yet 'signal transduction' is an is_a <br />
child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship<br />
as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow <br />
of time on the x axis, with the processes arranged according to the <br />
allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ).<br />
Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded <br />
by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. <br />
I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should <br />
really be initiated_by <br />
<br />
</pre><br />
<br />
==Chris's Reactome2GO analysis==<br />
<br />
3 cols of 3:<br />
<br />
Pathway/Process<br><br />
Initiating event<br><br />
Initial Event<br />
<br />
Each is split into 3 - reactome label, GO ID, GO label<br />
<br />
(Jen: I have checked this into cvs [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/xps/r2go-signaling.txt go/scratch/xps/r2go-signaling.txt])<br />
<br />
Here initial event is a reactome leaf node in P that has no preceding event in P. initiation event is the event preceding this one.<br />
<br />
I would expect that for any pathway that has the GO def "..generated as a consequence of a X receptor binding to..." to have something like "X receptor binding" (or something that entails this) as an initiating event and perhaps something like "X receptor activity" as the first event in the process. Is this too simplistic?<br />
<br />
<br />
<br />
==Cross-references to Reactome==<br />
<br />
Peter D'Eustachio is making a list of GO terms and Reactome terms that could be cross referenced. Once he has completed this he will pass the list along to be intergrated into the GO ontology file.<br />
<br />
==Glutamate pathway==<br />
<br />
Invite Anita Bandrowski to meet with the signaling working group to make new terms for the glutamate pathway and related areas. (abandrowski at ucsd.edu)<br />
<br />
==Documentation==<br />
<br />
Work with the signaling working group to try to produce the kind of docs that Chris is interested to see:<br />
<br />
[[image:signalingDocExample.pdf]]<br><br />
[[Image:signalingDocExample.jpg]]</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=File:SignalingDocExample.pdf&diff=24749File:SignalingDocExample.pdf2010-02-05T10:37:52Z<p>Jdeegan: uploaded a new version of "File:SignalingDocExample.pdf"</p>
<hr />
<div></div>Jdeeganhttps://wiki.geneontology.org/index.php?title=File:SignalingDocExample.pdf&diff=24748File:SignalingDocExample.pdf2010-02-05T10:37:13Z<p>Jdeegan: </p>
<hr />
<div></div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24747Signaling to do list2010-02-05T10:36:58Z<p>Jdeegan: </p>
<hr />
<div>==Logical definitions==<br />
<br />
Project from Chris Mungall:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from <br />
one location to another. The process terminates at the end of the <br />
sub-process of signal transduction, when the function of the cell <br />
has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process<br />
of signal transmission. This implies that signal transduction is <br />
part_of signal transmission. Yet 'signal transduction' is an is_a <br />
child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship<br />
as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow <br />
of time on the x axis, with the processes arranged according to the <br />
allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ).<br />
Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded <br />
by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. <br />
I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should <br />
really be initiated_by <br />
<br />
</pre><br />
<br />
==Chris's Reactome2GO analysis==<br />
<br />
3 cols of 3:<br />
<br />
Pathway/Process<br><br />
Initiating event<br><br />
Initial Event<br />
<br />
Each is split into 3 - reactome label, GO ID, GO label<br />
<br />
(Jen: I have checked this into cvs [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/xps/r2go-signaling.txt go/scratch/xps/r2go-signaling.txt])<br />
<br />
Here initial event is a reactome leaf node in P that has no preceding event in P. initiation event is the event preceding this one.<br />
<br />
I would expect that for any pathway that has the GO def "..generated as a consequence of a X receptor binding to..." to have something like "X receptor binding" (or something that entails this) as an initiating event and perhaps something like "X receptor activity" as the first event in the process. Is this too simplistic?<br />
<br />
<br />
<br />
==Cross-references to Reactome==<br />
<br />
Peter D'Eustachio is making a list of GO terms and Reactome terms that could be cross referenced. Once he has completed this he will pass the list along to be intergrated into the GO ontology file.<br />
<br />
==Glutamate pathway==<br />
<br />
Invite Anita Bandrowski to meet with the signaling working group to make new terms for the glutamate pathway and related areas. (abandrowski at ucsd.edu)<br />
<br />
==Documentation==<br />
<br />
Work with the signaling working group to try to produce the kind of docs that Chris is interested to see:<br />
<br />
[[image:signalingDocExample.pdf]]</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_demo_February_2010&diff=24746Signaling demo February 20102010-02-05T10:34:36Z<p>Jdeegan: </p>
<hr />
<div>The signaling working group gave a demo of the new graph to all from the consortium who wished to attend. We also had some outside experts to view the graph and in all it was about 30 people watching on webex and listening on the conference line. <br />
<br />
Many good questions were asked and Suzanna Lewis raised a question about splitting the part_of and is_a graph into different hierarchies by use of grouping terms rather than just different relationships. This question will be taken on to the managers' call as this style of work is common throughout the process ontology. <br />
<br />
One new outside expert has agreed to join the group as she has a great deal of knowledge of the glutamate signaling pathway and will be able to help to develop a really good ontology structure. She is Anita Bandrowski (abandrowski at ucsd.edu). <br />
<br />
The conclusions of the meeting were:<br />
<br />
a) Jennifer Deegan should commit the graph to the live repository in the week beginning 8th February 2010.<br><br />
b) Jennifer Deegan should write some documentation on the standard structures.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_demo_February_2010&diff=24745Signaling demo February 20102010-02-05T10:33:12Z<p>Jdeegan: Created page with 'The signaling working group gave a demo of the new graph to all from the consortium who wished to attend. We also had some outside experts to view the graph and in all it was abo…'</p>
<hr />
<div>The signaling working group gave a demo of the new graph to all from the consortium who wished to attend. We also had some outside experts to view the graph and in all it was about 30 people watching on webex and listening on the conference line. <br />
<br />
Many good questions were asked and Suzanna Lewis raised a question about splitting the part_of and is_a graph into different hierarchies by use of grouping terms rather than just different relationships. This question will be taken on to the managers' call as this style of work is common throughout the process ontology. <br />
<br />
One new outside expert has agreed to join the group as she has a great deal of knowledge of the glutamate signaling pathway and will be able to help to develop a really good ontology structure. She is Anita Bandrowski (abandrowski at ucsd.edu). <br />
<br />
The conclusions of the meeting were:<br />
<br />
a) Jennifer Deegan should commit the graph to the live repository in the week beginning 8th February 2010.<br />
b) Jennifer Deegan should write some documentation on the standard structures.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling&diff=24744Signaling2010-02-05T10:26:53Z<p>Jdeegan: </p>
<hr />
<div>Mailing list: signaling at genome.stanford.edu<br />
<br />
Sign up at: http://fafner.stanford.edu/mailman/listinfo/signaling<br />
<br />
[[Signaling Metrics]]<br />
<br />
==Signaling on Sourceforge==<br />
<br />
There are a large number of [[Signaling sourceforge items | signaling items]] awaiting attention on the sourceforge tracker. <br />
If you have an item that is not listed here then please feel free to add it. <br />
<br />
==Community ideas==<br />
<br />
If you have particular areas of expertise in signaling, or have general suggestions on how the terms could be improved then please add your name and brief details on the [[Signaling - pointers from the community | Community Input]] page<br />
<br />
==Text book views of signaling==<br />
<br />
Notes on general views of signaling from the standard text books are noted below.<br />
<br />
[[Signaling text book summary | Molecular Biology of the Cell]]<br />
<br />
[http://www.sabiosciences.com/pathwaycentral.php Signaling diagrams]<br />
<br />
[http://www.abcam.com/index.html?pageconfig=resource&rid=10723&pid=10628 More signaling diagrams]<br />
<br />
==Documentation on signaling in GO==<br />
<br />
Below are some attempts to document possible new signaling structures. Plese feel free to add your own suggested standard structures. <br />
<br />
[[Signaling ontology structure documentation]]<br />
<br />
==Discussion so far==<br />
<br />
Read about the discussions of signaling from [[Signaling Meeting Minutes April 2008 - | April 2008]] until July 2009.<br />
<br />
Read about the discussions of signaling from [[Signaling Meeting Minutes July 2009 | July 2009]].<br />
<br />
Read about the discussions of signaling from [[Signaling Meeting Minutes November 2009 | November 2009]].<br />
<br />
Read about the discussions of signaling from [[Signaling Meeting Minutes December 2009 | December 2009]].<br />
<br />
Read about the discussions of signaling from [[Signaling Meeting Minutes January 2010 | January 2010]].<br />
<br />
[[Signaling Proposal January 2010 | Proposal circulated via the GO list]].<br />
<br />
[[Signaling demo February 2010]]<br />
<br />
[[Signaling to do list]]<br />
<br />
==Signaling pathways, and the processes they regulate==<br />
<br />
We are collecting information on [[Signaling pathways, and the processes they regulate]]. If you are able to fill in any details then this would be greatly appreciated.<br />
<br />
==Some other ideas in progress==<br />
<br />
[[Signaling branch file]]<br />
<br />
[[Multi-organism process signaling modulation terms]]<br />
<br />
[[EBI signaling meeting 2009]] <br />
<br />
[[Draft organization of ideas]]<br />
<br />
<br />
[[Category:Ontology]]</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Part_10&diff=24678Taxon-GO Checks and Commentary - Part 102010-02-04T16:02:20Z<p>Jdeegan: Created page with 'Feedback from AgBase.'</p>
<hr />
<div>Feedback from AgBase.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon_Main_Page&diff=24677Taxon Main Page2010-02-04T16:02:07Z<p>Jdeegan: </p>
<hr />
<div>[[Manuscript of taxon checking system paper]]<br />
<br />
[[Taxon Trigger File Metrics]]<br />
<br />
[[Proposal 2007]]<br />
<br />
[[Taxon-GO Implementation April 2008 onwards]]<br />
<br />
[[Taxon-GO Implementation April 2009 onwards]]<br />
<br />
[[Taxon-GO Checks and Commentary - Part 1]] - GOA and others<br />
<br />
[[Taxon-GO Checks and Commentary - Part 2]] - FlyBase<br />
<br />
[[Taxon-GO Checks and Commentary - Part 3]] - GOA<br />
<br />
[[Taxon-GO Checks and Commentary - Part 4]] - Viruses<br />
<br />
[[Taxon-GO Checks and Commentary - Part 5]] - MGI, ZFIN and SGD<br />
<br />
[[Taxon-GO Checks and Commentary - Part 6]] - TAIR, RGD and EcoCyc<br />
<br />
[[Taxon-GO Checks and Commentary - Part 7]] - WormBase<br />
<br />
[[Taxon-GO Checks and Commentary - Part 8]] - submission via SourceForge<br />
<br />
[[Taxon-GO Checks and Commentary - Response to GOA - Part 5]]<br />
<br />
[[Taxon-GO Checks and Commentary - Part 9]] - GOA<br />
<br />
[[Taxon-GO Checks and Commentary - Part 10]] - AgBase<br />
<br />
[[Resolving redundancies in taxon links]]<br />
<br />
[[Taxon file location in cvs]]<br />
<br />
[[Union term id space]]<br />
<br />
[[To Do List - Taxon checks]]<br />
<br />
[[Are Multi-organism process and cellular process disjoint?]]<br />
<br />
<br />
[[Taxon Editing Workflow]] up until 12th June 2009<br />
<br />
[[Taxon Editing Workflow after 12th June 2009]]<br />
<br />
[[GAF_Taxonomy_Reasoning]]<br />
<br />
[[Category:Taxon]]</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=To_Do_List_-_Taxon_checks&diff=24590To Do List - Taxon checks2010-02-02T10:52:18Z<p>Jdeegan: </p>
<hr />
<div>==Ontology questions shown by GOA response to inconsistency file==<br />
<br />
<br />
<br />
*In the cross product files it would be better if I could just connect chloroplast and mitochondrion to the appropriate taxa so I don't need to make individual links to terms like id: GO:0010368 name: chloroplast isoamylase complex<br />
<br />
* Classify cell types by species specificity so we also get all GO terms with cross products to these terms: [[Taxon-GO_Implementation_April_2008_onwards#Cross_Product_files]]</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24550Signaling to do list2010-02-01T10:31:55Z<p>Jdeegan: </p>
<hr />
<div>==Logical definitions==<br />
<br />
Project from Chris Mungall:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from <br />
one location to another. The process terminates at the end of the <br />
sub-process of signal transduction, when the function of the cell <br />
has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process<br />
of signal transmission. This implies that signal transduction is <br />
part_of signal transmission. Yet 'signal transduction' is an is_a <br />
child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship<br />
as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow <br />
of time on the x axis, with the processes arranged according to the <br />
allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ).<br />
Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded <br />
by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. <br />
I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should <br />
really be initiated_by <br />
<br />
</pre><br />
<br />
==Chris's Reactome2GO analysis==<br />
<br />
3 cols of 3:<br />
<br />
Pathway/Process<br><br />
Initiating event<br><br />
Initial Event<br />
<br />
Each is split into 3 - reactome label, GO ID, GO label<br />
<br />
(Jen: I have checked this into cvs [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/xps/r2go-signaling.txt go/scratch/xps/r2go-signaling.txt])<br />
<br />
Here initial event is a reactome leaf node in P that has no preceding event in P. initiation event is the event preceding this one.<br />
<br />
I would expect that for any pathway that has the GO def "..generated as a consequence of a X receptor binding to..." to have something like "X receptor binding" (or something that entails this) as an initiating event and perhaps something like "X receptor activity" as the first event in the process. Is this too simplistic?<br />
<br />
<br />
<br />
==Cross-references to Reactome==<br />
<br />
Peter D'Eustachio is making a list of GO terms and Reactome terms that could be cross referenced. Once he has completed this he will pass the list along to be intergrated into the GO ontology file.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24549Signaling to do list2010-02-01T10:31:42Z<p>Jdeegan: </p>
<hr />
<div>==Logical definitions==<br />
<br />
Project from Chris Mungall:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from <br />
one location to another. The process terminates at the end of the <br />
sub-process of signal transduction, when the function of the cell <br />
has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process<br />
of signal transmission. This implies that signal transduction is <br />
part_of signal transmission. Yet 'signal transduction' is an is_a <br />
child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship<br />
as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow <br />
of time on the x axis, with the processes arranged according to the <br />
allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ).<br />
Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded <br />
by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. <br />
I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should <br />
really be initiated_by <br />
<br />
</pre><br />
<br />
===Chris's Reactome2GO analysis===<br />
<br />
3 cols of 3:<br />
<br />
Pathway/Process<br><br />
Initiating event<br><br />
Initial Event<br />
<br />
Each is split into 3 - reactome label, GO ID, GO label<br />
<br />
(Jen: I have checked this into cvs [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/xps/r2go-signaling.txt go/scratch/xps/r2go-signaling.txt])<br />
<br />
Here initial event is a reactome leaf node in P that has no preceding event in P. initiation event is the event preceding this one.<br />
<br />
I would expect that for any pathway that has the GO def "..generated as a consequence of a X receptor binding to..." to have something like "X receptor binding" (or something that entails this) as an initiating event and perhaps something like "X receptor activity" as the first event in the process. Is this too simplistic?<br />
<br />
<br />
<br />
==Cross-references to Reactome==<br />
<br />
Peter D'Eustachio is making a list of GO terms and Reactome terms that could be cross referenced. Once he has completed this he will pass the list along to be intergrated into the GO ontology file.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24548Signaling to do list2010-02-01T10:26:21Z<p>Jdeegan: </p>
<hr />
<div>==Logical definitions==<br />
<br />
Project from Chris Mungall:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from <br />
one location to another. The process terminates at the end of the <br />
sub-process of signal transduction, when the function of the cell <br />
has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process<br />
of signal transmission. This implies that signal transduction is <br />
part_of signal transmission. Yet 'signal transduction' is an is_a <br />
child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship<br />
as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow <br />
of time on the x axis, with the processes arranged according to the <br />
allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ).<br />
Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded <br />
by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. <br />
I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should <br />
really be initiated_by <br />
<br />
</pre><br />
<br />
===Chris's analysis===<br />
<br />
3 cols of 3:<br />
<br />
Pathway/Process<br><br />
Initiating event<br><br />
Initial Event<br />
<br />
Each is split into 3 - reactome label, GO ID, GO label<br />
<br />
(Jen: I have checked this into cvs [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/xps/r2go-signaling.txt go/scratch/xps/r2go-signaling.txt])<br />
<br />
Here initial event is a reactome leaf node in P that has no preceding event in P. initiation event is the event preceding this one.<br />
<br />
I would expect that for any pathway that has the GO def "..generated as a consequence of a X receptor binding to..." to have something like "X receptor binding" (or something that entails this) as an initiating event and perhaps something like "X receptor activity" as the first event in the process. Is this too simplistic?<br />
<br />
<br />
<br />
==Cross-references to Reactome==<br />
<br />
Peter D'Eustachio is making a list of GO terms and Reactome terms that could be cross referenced. Once he has completed this he will pass the list along to be intergrated into the GO ontology file.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24547Signaling to do list2010-02-01T10:17:56Z<p>Jdeegan: </p>
<hr />
<div>==Logical definitions==<br />
<br />
Project from Chris Mungall:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from <br />
one location to another. The process terminates at the end of the <br />
sub-process of signal transduction, when the function of the cell <br />
has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process<br />
of signal transmission. This implies that signal transduction is <br />
part_of signal transmission. Yet 'signal transduction' is an is_a <br />
child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship<br />
as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow <br />
of time on the x axis, with the processes arranged according to the <br />
allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ).<br />
Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded <br />
by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. <br />
I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should <br />
really be initiated_by <br />
<br />
</pre><br />
<br />
===Chris's analysis===<br />
<br />
3 cols of 3:<br />
<br />
Pathway/Process<br><br />
Initiating event<br><br />
Initial Event<br />
<br />
Each is split into 3 - reactome label, GO ID, GO label<br />
<br />
Here initial event is a reactome leaf node in P that has no preceding event in P. initiation event is the event preceding this one.<br />
<br />
I would expect that for any pathway that has the GO def "..generated as a consequence of a X receptor binding to..." to have something like "X receptor binding" (or something that entails this) as an initiating event and perhaps something like "X receptor activity" as the first event in the process. Is this too simplistic?<br />
<br />
[[File:r2go-signaling1.xls]]<br />
<br />
==Cross-references to Reactome==<br />
<br />
Peter D'Eustachio is making a list of GO terms and Reactome terms that could be cross referenced. Once he has completed this he will pass the list along to be intergrated into the GO ontology file.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24546Signaling to do list2010-02-01T10:11:32Z<p>Jdeegan: </p>
<hr />
<div>==Logical definitions==<br />
<br />
Project from Chris Mungall:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from <br />
one location to another. The process terminates at the end of the <br />
sub-process of signal transduction, when the function of the cell <br />
has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process<br />
of signal transmission. This implies that signal transduction is <br />
part_of signal transmission. Yet 'signal transduction' is an is_a <br />
child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship<br />
as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow <br />
of time on the x axis, with the processes arranged according to the <br />
allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ).<br />
Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded <br />
by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. <br />
I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should <br />
really be initiated_by <br />
<br />
</pre><br />
<br />
===Chris's analysis===<br />
<br />
3 cols of 3:<br />
<br />
Pathway/Process<br><br />
Initiating event<br><br />
Initial Event<br />
<br />
Each is split into 3 - reactome label, GO ID, GO label<br />
<br />
Here initial event is a reactome leaf node in P that has no preceding event in P. initiation event is the event preceding this one.<br />
<br />
I would expect that for any pathway that has the GO def "..generated as a consequence of a X receptor binding to..." to have something like "X receptor binding" (or something that entails this) as an initiating event and perhaps something like "X receptor activity" as the first event in the process. Is this too simplistic?<br />
<br />
[[File:r2go-signaling.xls]]<br />
<br />
==Cross-references to Reactome==<br />
<br />
Peter D'Eustachio is making a list of GO terms and Reactome terms that could be cross referenced. Once he has completed this he will pass the list along to be intergrated into the GO ontology file.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24545Signaling to do list2010-02-01T10:10:05Z<p>Jdeegan: </p>
<hr />
<div>==Logical definitions==<br />
<br />
Project from Chris Mungall:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from <br />
one location to another. The process terminates at the end of the <br />
sub-process of signal transduction, when the function of the cell <br />
has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process<br />
of signal transmission. This implies that signal transduction is <br />
part_of signal transmission. Yet 'signal transduction' is an is_a <br />
child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship<br />
as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow <br />
of time on the x axis, with the processes arranged according to the <br />
allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ).<br />
Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded <br />
by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. <br />
I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should <br />
really be initiated_by <br />
<br />
</pre><br />
<br />
===Chris's analysis===<br />
<br />
3 cols of 3:<br />
<br />
Pathway/Process<br><br />
Initiating event<br><br />
Initial Event<br />
<br />
Each is split into 3 - reactome label, GO ID, GO label<br />
<br />
Here initial event is a reactome leaf node in P that has no preceding event in P. initiation event is the event preceding this one.<br />
<br />
I would expect that for any pathway that has the GO def "..generated as a consequence of a X receptor binding to..." to have something like "X receptor binding" (or something that entails this) as an initiating event and perhaps something like "X receptor activity" as the first event in the process. Is this too simplistic?<br />
<br />
[[File:r2go-signaling.txt]]<br />
<br />
==Cross-references to Reactome==<br />
<br />
Peter D'Eustachio is making a list of GO terms and Reactome terms that could be cross referenced. Once he has completed this he will pass the list along to be intergrated into the GO ontology file.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24544Signaling to do list2010-02-01T10:09:24Z<p>Jdeegan: </p>
<hr />
<div>==Logical definitions==<br />
<br />
Project from Chris Mungall:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from <br />
one location to another. The process terminates at the end of the <br />
sub-process of signal transduction, when the function of the cell <br />
has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process<br />
of signal transmission. This implies that signal transduction is <br />
part_of signal transmission. Yet 'signal transduction' is an is_a <br />
child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship<br />
as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow <br />
of time on the x axis, with the processes arranged according to the <br />
allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ).<br />
Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded <br />
by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. <br />
I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should <br />
really be initiated_by <br />
<br />
</pre><br />
<br />
===Chris's analysis===<br />
<br />
3 cols of 3:<br />
<br />
Pathway/Process<br><br />
Initiating event<br><br />
Initial Event<br />
<br />
Each is split into 3 - reactome label, GO ID, GO label<br />
<br />
Here initial event is a reactome leaf node in P that has no preceding event in P. initiation event is the event preceding this one.<br />
<br />
I would expect that for any pathway that has the GO def "..generated as a consequence of a X receptor binding to..." to have something like "X receptor binding" (or something that entails this) as an initiating event and perhaps something like "X receptor activity" as the first event in the process. Is this too simplistic?<br />
<br />
<pre><br />
<br />
<br />
</pre><br />
<br />
<br />
==Cross-references to Reactome==<br />
<br />
Peter D'Eustachio is making a list of GO terms and Reactome terms that could be cross referenced. Once he has completed this he will pass the list along to be intergrated into the GO ontology file.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24541Signaling to do list2010-02-01T09:57:35Z<p>Jdeegan: </p>
<hr />
<div>==Logical definitions==<br />
<br />
Project from Chris Mungall:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from <br />
one location to another. The process terminates at the end of the <br />
sub-process of signal transduction, when the function of the cell <br />
has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process<br />
of signal transmission. This implies that signal transduction is <br />
part_of signal transmission. Yet 'signal transduction' is an is_a <br />
child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship<br />
as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow <br />
of time on the x axis, with the processes arranged according to the <br />
allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ).<br />
Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded <br />
by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. <br />
I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should <br />
really be initiated_by <br />
<br />
</pre><br />
<br />
==Cross-references to Reactome==<br />
<br />
Peter D'Eustachio is making a list of GO terms and Reactome terms that could be cross referenced. Once he has completed this he will pass the list along to be intergrated into the GO ontology file.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24540Signaling to do list2010-02-01T09:56:07Z<p>Jdeegan: </p>
<hr />
<div>Project from Chris:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from <br />
one location to another. The process terminates at the end of the <br />
sub-process of signal transduction, when the function of the cell <br />
has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process<br />
of signal transmission. This implies that signal transduction is <br />
part_of signal transmission. Yet 'signal transduction' is an is_a <br />
child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship<br />
as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow <br />
of time on the x axis, with the processes arranged according to the <br />
allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ).<br />
Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded <br />
by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. <br />
I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should <br />
really be initiated_by <br />
<br />
</pre></div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling_to_do_list&diff=24539Signaling to do list2010-02-01T09:54:08Z<p>Jdeegan: Created page with 'Project from Chris: <pre> >> (4) 'signal transmission' is defined as: >> "The process whereby a signal is released and/or conveyed from one location to another. The process ter…'</p>
<hr />
<div>Project from Chris:<br />
<br />
<pre><br />
<br />
>> (4) 'signal transmission' is defined as:<br />
>> "The process whereby a signal is released and/or conveyed from one location to another. The process terminates at the end of the sub-process of signal transduction, when the function of the cell has been altered as a consequence of receipt of the signal."<br />
>> So, the definition says that signal transduction is a sub-process of signal transmission. This implies that signal transduction is part_of signal transmission. Yet 'signal transduction' is an is_a child of signal transmission. Which is correct?<br />
><br />
> I think they are both correct. I am going to leave the relationship as is_a. We could follow this up in a separate thread if you'd like to discuss it.<br />
<br />
This is a bit worrying.<br />
<br />
What I would really appreciate is a simple diagram showing the flow of time on the x axis, with the processes arranged according to the allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ). Looking at signaling3.obo doesn't really tell me the changes.<br />
<br />
for example, is a receptor binding pathway always immediately preceded by receptor binding? (Reactome doesn't appear to be consistent here)<br />
<br />
I think we should get the logical definition template correct first. I have set up a file biological_process_xp_signaling.obo<br />
<br />
I used starts_with, which implies part_of, but I think this should really be initiated_by <br />
<br />
</pre></div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Signaling&diff=24538Signaling2010-02-01T09:53:29Z<p>Jdeegan: </p>
<hr />
<div>Mailing list: signaling at genome.stanford.edu<br />
<br />
Sign up at: http://fafner.stanford.edu/mailman/listinfo/signaling<br />
<br />
[[Signaling Metrics]]<br />
<br />
==Signaling on Sourceforge==<br />
<br />
There are a large number of [[Signaling sourceforge items | signaling items]] awaiting attention on the sourceforge tracker. <br />
If you have an item that is not listed here then please feel free to add it. <br />
<br />
==Community ideas==<br />
<br />
If you have particular areas of expertise in signaling, or have general suggestions on how the terms could be improved then please add your name and brief details on the [[Signaling - pointers from the community | Community Input]] page<br />
<br />
==Text book views of signaling==<br />
<br />
Notes on general views of signaling from the standard text books are noted below.<br />
<br />
[[Signaling text book summary | Molecular Biology of the Cell]]<br />
<br />
[http://www.sabiosciences.com/pathwaycentral.php Signaling diagrams]<br />
<br />
[http://www.abcam.com/index.html?pageconfig=resource&rid=10723&pid=10628 More signaling diagrams]<br />
<br />
==Documentation on signaling in GO==<br />
<br />
Below are some attempts to document possible new signaling structures. Plese feel free to add your own suggested standard structures. <br />
<br />
[[Signaling ontology structure documentation]]<br />
<br />
==Discussion so far==<br />
<br />
Read about the discussions of signaling from [[Signaling Meeting Minutes April 2008 - | April 2008]] until July 2009.<br />
<br />
Read about the discussions of signaling from [[Signaling Meeting Minutes July 2009 | July 2009]].<br />
<br />
Read about the discussions of signaling from [[Signaling Meeting Minutes November 2009 | November 2009]].<br />
<br />
Read about the discussions of signaling from [[Signaling Meeting Minutes December 2009 | December 2009]].<br />
<br />
Read about the discussions of signaling from [[Signaling Meeting Minutes January 2010 | January 2010]].<br />
<br />
[[Signaling Proposal January 2010 | Proposal circulated via the GO list]].<br />
<br />
[[Signaling to do list]]<br />
<br />
==Signaling pathways, and the processes they regulate==<br />
<br />
We are collecting information on [[Signaling pathways, and the processes they regulate]]. If you are able to fill in any details then this would be greatly appreciated.<br />
<br />
==Some other ideas in progress==<br />
<br />
[[Signaling branch file]]<br />
<br />
[[Multi-organism process signaling modulation terms]]<br />
<br />
[[EBI signaling meeting 2009]] <br />
<br />
[[Draft organization of ideas]]<br />
<br />
<br />
[[Category:Ontology]]</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Are_multi-organism_process_and_cellular_process_disjoint%3F&diff=24445Are multi-organism process and cellular process disjoint?2010-01-28T16:40:39Z<p>Jdeegan: </p>
<hr />
<div>==Proposal 1 - Multi-organism process and cellular process should no longer be disjoint==<br />
<br />
From examination of the taxon inconsistency file it would seem that these two processes are not disjoint in principle, though they currently are recorded as being disjoint in GO. <br />
<br />
* According to current thinking, the cellular process term covers processes occurring at the cellular level in a single organism. <br />
* Multi-organism process covers processes that involve more than one organism. <br />
* These two processes are considered disjoint (mutually exclusive), and so cannot have is_a children in common.<br />
<br />
So the question is, where do we put processes ocurring at the cellular level, and including multiple organisms? Examples are 'receptor mediated endocytosis of virus by host' and 'viral transcription'. The process 'receptor mediated endocytosis of virus by host' clearly happens at the cellular level but requires the participation of viral gene products, and so is a cellular multi-organism process. We cannot currently make the term 'cellular multi-organism process' because it would be an is_a child of both multi-organism process and cellular process. This is not allowed, as the two parent terms are disjoint. <br />
<br />
This stucture is not permitted as the two parent terms are disjoint:<br />
<br />
[i]cellular process<br />
---[i]cellular multi-organism process<br />
[i]multi-organism process<br />
---[i]cellular multi-organism process<br />
<br />
Somehow we have to decide whether to place 'receptor mediated endocytosis of virus by host' under cellular process or multi-organism process, but it doesn't make sense to choose, as it is clearly happening at the cellular level, and involves two organisms. <br />
<br />
Currently we have terms that should be descendents of cellular multi-organism process placed as descendents of cellular process, and they have virus annotations. As we start to make more virus annotations, it is inevitable that there will be more terms like this. Such terms are immediately flagged up if a taxon rule is made as follows:<br />
<br />
[Term]<br />
id: GO:0009987<br />
name: cellular process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
(Cellular organisms excludes viruses.)<br />
<br />
It would be helpful to resolve this problem at some point, but this can only be done if the multi-organism process and cellular process are no longer stipulated to be disjoint from one another.<br />
<br />
===Proposal 1===<br />
<br />
I would like to propose that the disjoint relationship between cellular process and multi-organism process be removed, and a child term cellular multi-organism process be created. <br />
<br />
==Proposal 2 - Direct or indirect viral annotations to cellular process should be allowed==<br />
<br />
Following on from the proposal above, if a viral annotation was made to a term such as 'receptor mediated endocytosis of virus by host' and then slimmed up to cellular process, then the annotation would be wrong according to current thinking. (Current GO community understanding is that cellular processes can only be carried out by gene products of cellular organisms, and viruses are not cellular organisms.) <br />
<br />
===Proposal 2===<br />
<br />
I would like to propose that the term cellular process should not be restricted to use only for annotation of gene products of cellular organisms, either in the taxon checking file or in the definition or established understanding of the term. With or without the acceptance of proposal 1, cellular process will still be an ancestor of terms such as 'receptor mediated endocytosis of virus by host' and so it will be as well that annotations should be able to be slimmed up to cellular process without being incorrect.<br />
<br />
==Comments==<br />
<br />
'''Midori''': "I think it would help Val quite a bit with the yeast mating (i.e. conjugation with cellular fusion)."<br><br />
<br><br />
'''Jane''': I think we do need to keep multi-organism processes disjoint with single-organism processes - at the moment cellular processes are always single organism so there isn't a problem. Otherwise I think we'll end up with oddities in slims etc. In the example you give, genes involved in multi-organism processes would end up slimmed to a cellular process parent - that might be very confusing.<br />
<br />
However, to keep them disjoint would lead to this sort of structure:<br />
<br />
single-organism process<br />
---[i] single-organism cellular process<br />
---[i] single-organism multicellular process<br />
multi-organism process<br />
---[i] multi-organism cellular process<br />
---[i] multi-organism multicellular process<br />
multicellular process<br />
---[i] multi-organism multicellular process<br />
---[i] single-organism multicellular process<br />
cellular process<br />
---[i] single-organism cellular process<br />
---[i] multi-organism cellular process<br />
<br />
which I'm not happy with either. I think this warrants more thought. I do see the problem though.<br />
<br />
Thread carries on on the go list:<br />
<br />
'''Re: [Go] disjoint proposal'''<br><br />
'''28/01/2010'''<br />
<br />
Concludes that in fact 'multi-organism process' was really intended to be 'multi-organism process occuring at the cellular, tissue, organ or organism level' whereas 'cellular process' was intended to be 'single organism process occurring at the cellular level'. <br />
<br />
This means that we need to come back to these terms and properly define them and then move the multi-organism processes out of under 'cellular process'.<br />
<br />
Later, others disagree and it is proposed to take this to the consortium meeting.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Ontology_Development&diff=24438Ontology Development2010-01-28T15:41:35Z<p>Jdeegan: </p>
<hr />
<div>This group's purpose is to ensure that the Gene Ontology represents biology in a way that is useful for gene product annotation of reference genomes and other MODs using the GO for annotation. The group serves as the link between biological knowledge that is gained from wet-bench scientists and the representation of that knowledge in the GO. Members of the group are responsible for reporting areas of the GO that need development and for suggesting changes and additions to the GO as needs arise. Members of the group serve as biological experts in domains that are covered by their organism. They are responsible for reviewing changes to be sure that they accurately reflect our current understanding of biology.<br />
<br />
==Administrative==<br />
*[[Ontology Development group summary]]<br />
*[[Meeting_minutes:_general_topics|Miscellaneous meeting minutes]]<br />
<br />
==Content Development ==<br />
===Priority ranking===<br />
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)<br />
*High Priority<br />
**Cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]<br />
***[[Cell cross-products]] (David, Jane, Tanya, Alex, Chris, others?)<br />
***[[XP:biological_process_xp_chebi |Chebi cross-products]] (David, Jane, Tanya, Chris, others?)<br />
**[[Cellular component processes]] (Jane, David, Midori, Val, ad hoc others)<br />
**[[Taxon and sensu|Taxon data]] (Note: sensu revamp complete) (Jen)<br />
**[[Function-Process Links]]<br />
***part_of links between function and process (David, Tanya)<br />
***has_part links between function and process (Harold, Jen)<br />
**[[Transporters]](Jen and community experts)<br />
**[[Metabolism |Filling in metabolism terms]] (Jane, David, Chris, Midori)<br />
**Generic [[GO slim overhaul]] (Jane, Val, others?)<br />
*Medium Priority<br />
**[[:Category:Content PAMGO|PAMGO collaboration]] (Jane)<br />
**[[Virus terms|Virus-related term overhaul]] (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh, Alexander Diehl & others)<br />
**IMG mapping (Jane)<br />
**[[Signaling |Signaling overhaul]] (Jen, Alex Diehl)<br />
**[[Transcription |Transcription & transcription factor activity overhaul]] (Karen)<br />
**[[Kidney Development]] (David, Midori, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)<br />
*Low priority<br />
**[[Response to drug]] (Jen)<br />
**Ion homeostasis ([https://sourceforge.net/tracker/func=detail&atid=440764&aid=1751898&group_id=36855| SF 1751898])<br />
**Cytokine receptor binding ([https://sourceforge.net/tracker/ufnc=detail&atid=440764&aid=1751924&group_id=36855| SF 1751924])<br />
**Peripheral nervous system development<br />
**Formation/assembly/biogenesis/etc. rationalization ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1733770&group_id=36855| SF 1733770])<br />
**[[Polyketide synthases]]<br />
<br />
===Timeline===<br />
====Current content work====<br />
*[[Virus terms|Virus-related term overhaul]] (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh & others)<br />
*[[Signaling |Signaling overhaul]]<br />
*[[Cellular component processes]] (Jane, David, Midori, Val, ad hoc others) - started summer 2008<br />
*[[Transcription |Transcription & transcription factor activity overhaul]] - started June 2008<br />
*[[Taxon and sensu|Taxon data]] <br />
*[[Transporters]] - Started Feb. 2007<br />
*[[Electron transport]]<br />
*IMG mapping<br />
*[[Function-Process Links]] - pilot projects begun Feb. 2008; first links added May 2009<br />
**kinases, phosphatases, transporters, and other 1:1- May/June 2009<br />
*[[Cell cross-products]] - TBD<br />
*[[Plant terms]]<br />
* Filling in [[metabolism]] terms - face-to-face meeting July 9, 2008<br />
* [[Notes on Sourceforge items in progress]]<br />
<br />
====Future content work====<br />
*Generic [[GO slim overhaul]] - summer 2009<br />
*Ion homeostasis ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1751898&group_id=36855| SF 1751898])<br />
*Cytokine receptor binding ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1751924&group_id=36855| SF 1751924])<br />
*[[Response to drug]]<br />
*Peripheral nervous system development<br />
*Formation/assembly/biogenesis/etc. rationalization ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1733770&group_id=36855| SF 1733770])<br />
*[[Polyketide synthases]]<br />
<br />
===[[Selected SourceForge links]]===<br />
<br />
===Completed content work===<br />
*[[:Category:Content PAMGO|PAMGO collaboration]], phase 2 (as of Jan. 2007)<br />
*[[Immunology Revisions]]<br />
*[[Central Nervous System Development]]<br />
*[[Isa-complete_BP|is_a complete biological process]]<br />
*[[:Category:Content PAMGO|PAMGO collaboration]], phase 1<br />
*Correct disjointness violations<br />
*[[RNA processing]]<br />
*[[Collaboration with MIT GO-Engineering]] - Manuscript written<br />
*[[Muscle Development]] - Started Feb. 2007; meeting July 2007; Done Oct 2007<br />
*[[Cardiovascular physiology/development]] - implemented Oct 2007<br />
*Make cc part_of tree complete (i.e. find homes for the children of 'unlocalized protein complex')<br />
*[[Sensu Main Page|Sensu revamp]]<br />
*[[Regulation Main Page]] live March 2008<br />
*Gene expression ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1418820&group_id=36855| SF 1418820])<br />
*[[Electron transport]]<br />
*[[Proteases |Peptidase & protease activity overhaul]] begun June 2008; essentially completed August 2008<br />
*[[SDB 2009]]<br />
*[[Function-Process Links]]<br />
**[[FP-regulates| regulates links between function and process]] (David, Tanya)<br />
*[[Morphogenesis]] (David, Tanya)<br />
*regulates links- Dec 2008 (David, Tanya)<br />
*[[Regulators |Regulator, activator and inhibitor MF terms]] (David, Tanya)<br />
*[[Chaperones]](completed by working group at Cambridge GOC meeting Sept. 2009)<br />
**[http://wiki.geneontology.org/index.php/Lung_Development Lung Development] (David, Jen, community experts)<br />
**[[Binding_terms_working_group|Binding]] discussion - mainly annotation issues, but with some ontology content points<br />
<br />
===Proposed content work===<br />
A list of topics that we propose to address, but for which a timeline has not been set<br />
<br />
*Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology. <br />
*Rework disjoint terms as [[http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F#Conclusion concluded in discussion on GO list]].<br />
<br />
<br />
==Other Ontology Development Group Activities==<br />
*[[GO Timeline|Ontology development timeline]] and [[Ontology_publishing_pipeline_2009|release pipeline]]<br />
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)<br />
*[[Tracker wishlist]]<br />
*[[Webinar Software Investigation]]<br />
*[[Content Meeting Documentation]]<br />
**[http://wiki.geneontology.org/index.php/Content_Meeting_Participants_Information| Content meeting participants' information]<br />
*[[Editor Guide]]<br />
*[[Ontology Documentation Drafts]] - for working on documentation of ontology content that will become part of the web-based documentation<br />
<br />
==Agenda Items==<br />
*[[Agenda items for next content conference call]]<br />
<br />
==Reports==<br />
Beginning with the November 2006 document, reports include two sections: the first focuses on ontology development work, and the second gives an overview of the rest of the GO Editorial Office staff activities (to avoid redundancy, the latter may cross-reference other management group reports). Reports issued earlier are not so divided, and have a GO Editorial Office-centric perspective, but do cover a substantial portion of the GOC's ontology development work.<br />
<br />
*November 2006-present [[Ontology_Development_reports|Combined Ontology Development and GO Editorial Office reports]]<br />
*July 2005-October 2006 [[GO Editorial Office reports]]<br />
<br />
==GO Clinics==<br />
<br />
*[[GO clinic late 2009]]<br />
*[[GO clinic spring 2010]]<br />
<br />
<br />
[[Category:Ontology]]</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Ontology_Development&diff=24437Ontology Development2010-01-28T15:40:33Z<p>Jdeegan: </p>
<hr />
<div>This group's purpose is to ensure that the Gene Ontology represents biology in a way that is useful for gene product annotation of reference genomes and other MODs using the GO for annotation. The group serves as the link between biological knowledge that is gained from wet-bench scientists and the representation of that knowledge in the GO. Members of the group are responsible for reporting areas of the GO that need development and for suggesting changes and additions to the GO as needs arise. Members of the group serve as biological experts in domains that are covered by their organism. They are responsible for reviewing changes to be sure that they accurately reflect our current understanding of biology.<br />
<br />
==Administrative==<br />
*[[Ontology Development group summary]]<br />
*[[Meeting_minutes:_general_topics|Miscellaneous meeting minutes]]<br />
<br />
==Content Development ==<br />
===Priority ranking===<br />
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)<br />
*High Priority<br />
**Cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]<br />
***[[Cell cross-products]] (David, Jane, Tanya, Alex, Chris, others?)<br />
***[[XP:biological_process_xp_chebi |Chebi cross-products]] (David, Jane, Tanya, Chris, others?)<br />
**[[Cellular component processes]] (Jane, David, Midori, Val, ad hoc others)<br />
**[[Taxon and sensu|Taxon data]] (Note: sensu revamp complete) (Jen)<br />
**[[Function-Process Links]]<br />
***part_of links between function and process (David, Tanya)<br />
***has_part links between function and process (Harold, Jen)<br />
**[[Transporters]](Jen and community experts)<br />
**[[Metabolism |Filling in metabolism terms]] (Jane, David, Chris, Midori)<br />
**Generic [[GO slim overhaul]] (Jane, Val, others?)<br />
*Medium Priority<br />
**[[:Category:Content PAMGO|PAMGO collaboration]] (Jane)<br />
**[[Virus terms|Virus-related term overhaul]] (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh, Alexander Diehl & others)<br />
**IMG mapping (Jane)<br />
**[[Signaling |Signaling overhaul]] (Jen, Alex Diehl)<br />
**[[Transcription |Transcription & transcription factor activity overhaul]] (Karen)<br />
**[[Kidney Development]] (David, Midori, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)<br />
*Low priority<br />
**[[Response to drug]] (Jen)<br />
**Ion homeostasis ([https://sourceforge.net/tracker/func=detail&atid=440764&aid=1751898&group_id=36855| SF 1751898])<br />
**Cytokine receptor binding ([https://sourceforge.net/tracker/ufnc=detail&atid=440764&aid=1751924&group_id=36855| SF 1751924])<br />
**Peripheral nervous system development<br />
**Formation/assembly/biogenesis/etc. rationalization ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1733770&group_id=36855| SF 1733770])<br />
**[[Polyketide synthases]]<br />
<br />
===Timeline===<br />
====Current content work====<br />
*[[Virus terms|Virus-related term overhaul]] (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh & others)<br />
*[[Signaling |Signaling overhaul]]<br />
*[[Cellular component processes]] (Jane, David, Midori, Val, ad hoc others) - started summer 2008<br />
*[[Transcription |Transcription & transcription factor activity overhaul]] - started June 2008<br />
*[[Taxon and sensu|Taxon data]] <br />
*[[Transporters]] - Started Feb. 2007<br />
*[[Electron transport]]<br />
*IMG mapping<br />
*[[Function-Process Links]] - pilot projects begun Feb. 2008; first links added May 2009<br />
**kinases, phosphatases, transporters, and other 1:1- May/June 2009<br />
*[[Cell cross-products]] - TBD<br />
*[[Plant terms]]<br />
* Filling in [[metabolism]] terms - face-to-face meeting July 9, 2008<br />
* [[Notes on Sourceforge items in progress]]<br />
<br />
====Future content work====<br />
*Generic [[GO slim overhaul]] - summer 2009<br />
*Ion homeostasis ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1751898&group_id=36855| SF 1751898])<br />
*Cytokine receptor binding ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1751924&group_id=36855| SF 1751924])<br />
*[[Response to drug]]<br />
*Peripheral nervous system development<br />
*Formation/assembly/biogenesis/etc. rationalization ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1733770&group_id=36855| SF 1733770])<br />
*[[Polyketide synthases]]<br />
<br />
===[[Selected SourceForge links]]===<br />
<br />
===Completed content work===<br />
*[[:Category:Content PAMGO|PAMGO collaboration]], phase 2 (as of Jan. 2007)<br />
*[[Immunology Revisions]]<br />
*[[Central Nervous System Development]]<br />
*[[Isa-complete_BP|is_a complete biological process]]<br />
*[[:Category:Content PAMGO|PAMGO collaboration]], phase 1<br />
*Correct disjointness violations<br />
*[[RNA processing]]<br />
*[[Collaboration with MIT GO-Engineering]] - Manuscript written<br />
*[[Muscle Development]] - Started Feb. 2007; meeting July 2007; Done Oct 2007<br />
*[[Cardiovascular physiology/development]] - implemented Oct 2007<br />
*Make cc part_of tree complete (i.e. find homes for the children of 'unlocalized protein complex')<br />
*[[Sensu Main Page|Sensu revamp]]<br />
*[[Regulation Main Page]] live March 2008<br />
*Gene expression ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1418820&group_id=36855| SF 1418820])<br />
*[[Electron transport]]<br />
*[[Proteases |Peptidase & protease activity overhaul]] begun June 2008; essentially completed August 2008<br />
*[[SDB 2009]]<br />
*[[Function-Process Links]]<br />
**[[FP-regulates| regulates links between function and process]] (David, Tanya)<br />
*[[Morphogenesis]] (David, Tanya)<br />
*regulates links- Dec 2008 (David, Tanya)<br />
*[[Regulators |Regulator, activator and inhibitor MF terms]] (David, Tanya)<br />
*[[Chaperones]](completed by working group at Cambridge GOC meeting Sept. 2009)<br />
**[http://wiki.geneontology.org/index.php/Lung_Development Lung Development] (David, Jen, community experts)<br />
**[[Binding_terms_working_group|Binding]] discussion - mainly annotation issues, but with some ontology content points<br />
<br />
===Proposed content work===<br />
A list of topics that we propose to address, but for which a timeline has not been set<br />
<br />
*Revamp embryonc and post-emrbyonic terms to be logically defined with cross products. <br />
*Rework disjoint terms as [[http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F#Conclusion concluded]].<br />
<br />
<br />
==Other Ontology Development Group Activities==<br />
*[[GO Timeline|Ontology development timeline]] and [[Ontology_publishing_pipeline_2009|release pipeline]]<br />
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)<br />
*[[Tracker wishlist]]<br />
*[[Webinar Software Investigation]]<br />
*[[Content Meeting Documentation]]<br />
**[http://wiki.geneontology.org/index.php/Content_Meeting_Participants_Information| Content meeting participants' information]<br />
*[[Editor Guide]]<br />
*[[Ontology Documentation Drafts]] - for working on documentation of ontology content that will become part of the web-based documentation<br />
<br />
==Agenda Items==<br />
*[[Agenda items for next content conference call]]<br />
<br />
==Reports==<br />
Beginning with the November 2006 document, reports include two sections: the first focuses on ontology development work, and the second gives an overview of the rest of the GO Editorial Office staff activities (to avoid redundancy, the latter may cross-reference other management group reports). Reports issued earlier are not so divided, and have a GO Editorial Office-centric perspective, but do cover a substantial portion of the GOC's ontology development work.<br />
<br />
*November 2006-present [[Ontology_Development_reports|Combined Ontology Development and GO Editorial Office reports]]<br />
*July 2005-October 2006 [[GO Editorial Office reports]]<br />
<br />
==GO Clinics==<br />
<br />
*[[GO clinic late 2009]]<br />
*[[GO clinic spring 2010]]<br />
<br />
<br />
[[Category:Ontology]]</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Are_multi-organism_process_and_cellular_process_disjoint%3F&diff=24436Are multi-organism process and cellular process disjoint?2010-01-28T15:38:53Z<p>Jdeegan: </p>
<hr />
<div>==Proposal 1 - Multi-organism process and cellular process should no longer be disjoint==<br />
<br />
From examination of the taxon inconsistency file it would seem that these two processes are not disjoint in principle, though they currently are recorded as being disjoint in GO. <br />
<br />
* According to current thinking, the cellular process term covers processes occurring at the cellular level in a single organism. <br />
* Multi-organism process covers processes that involve more than one organism. <br />
* These two processes are considered disjoint (mutually exclusive), and so cannot have is_a children in common.<br />
<br />
So the question is, where do we put processes ocurring at the cellular level, and including multiple organisms? Examples are 'receptor mediated endocytosis of virus by host' and 'viral transcription'. The process 'receptor mediated endocytosis of virus by host' clearly happens at the cellular level but requires the participation of viral gene products, and so is a cellular multi-organism process. We cannot currently make the term 'cellular multi-organism process' because it would be an is_a child of both multi-organism process and cellular process. This is not allowed, as the two parent terms are disjoint. <br />
<br />
This stucture is not permitted as the two parent terms are disjoint:<br />
<br />
[i]cellular process<br />
---[i]cellular multi-organism process<br />
[i]multi-organism process<br />
---[i]cellular multi-organism process<br />
<br />
Somehow we have to decide whether to place 'receptor mediated endocytosis of virus by host' under cellular process or multi-organism process, but it doesn't make sense to choose, as it is clearly happening at the cellular level, and involves two organisms. <br />
<br />
Currently we have terms that should be descendents of cellular multi-organism process placed as descendents of cellular process, and they have virus annotations. As we start to make more virus annotations, it is inevitable that there will be more terms like this. Such terms are immediately flagged up if a taxon rule is made as follows:<br />
<br />
[Term]<br />
id: GO:0009987<br />
name: cellular process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
(Cellular organisms excludes viruses.)<br />
<br />
It would be helpful to resolve this problem at some point, but this can only be done if the multi-organism process and cellular process are no longer stipulated to be disjoint from one another.<br />
<br />
===Proposal 1===<br />
<br />
I would like to propose that the disjoint relationship between cellular process and multi-organism process be removed, and a child term cellular multi-organism process be created. <br />
<br />
==Proposal 2 - Direct or indirect viral annotations to cellular process should be allowed==<br />
<br />
Following on from the proposal above, if a viral annotation was made to a term such as 'receptor mediated endocytosis of virus by host' and then slimmed up to cellular process, then the annotation would be wrong according to current thinking. (Current GO community understanding is that cellular processes can only be carried out by gene products of cellular organisms, and viruses are not cellular organisms.) <br />
<br />
===Proposal 2===<br />
<br />
I would like to propose that the term cellular process should not be restricted to use only for annotation of gene products of cellular organisms, either in the taxon checking file or in the definition or established understanding of the term. With or without the acceptance of proposal 1, cellular process will still be an ancestor of terms such as 'receptor mediated endocytosis of virus by host' and so it will be as well that annotations should be able to be slimmed up to cellular process without being incorrect.<br />
<br />
==Comments==<br />
<br />
'''Midori''': "I think it would help Val quite a bit with the yeast mating (i.e. conjugation with cellular fusion)."<br><br />
<br><br />
'''Jane''': I think we do need to keep multi-organism processes disjoint with single-organism processes - at the moment cellular processes are always single organism so there isn't a problem. Otherwise I think we'll end up with oddities in slims etc. In the example you give, genes involved in multi-organism processes would end up slimmed to a cellular process parent - that might be very confusing.<br />
<br />
However, to keep them disjoint would lead to this sort of structure:<br />
<br />
single-organism process<br />
---[i] single-organism cellular process<br />
---[i] single-organism multicellular process<br />
multi-organism process<br />
---[i] multi-organism cellular process<br />
---[i] multi-organism multicellular process<br />
multicellular process<br />
---[i] multi-organism multicellular process<br />
---[i] single-organism multicellular process<br />
cellular process<br />
---[i] single-organism cellular process<br />
---[i] multi-organism cellular process<br />
<br />
which I'm not happy with either. I think this warrants more thought. I do see the problem though.<br />
<br />
Thread carries on on the go list:<br />
<br />
'''Re: [Go] disjoint proposal'''<br><br />
'''28/01/2010'''<br />
<br />
==Conclusion==<br />
<br />
Concludes that in fact 'multi-organism process' was really intended to be 'multi-organism process occuring at the cellular, tissue, organ or organism level' whereas 'cellular process' was intended to be 'single organism process occurring at the cellular level'. <br />
<br />
This means that we need to come back to these terms and properly define them and then move the multi-organism processes out of under 'cellular process'.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Are_multi-organism_process_and_cellular_process_disjoint%3F&diff=24435Are multi-organism process and cellular process disjoint?2010-01-28T15:36:40Z<p>Jdeegan: </p>
<hr />
<div>==Proposal 1 - Multi-organism process and cellular process should no longer be disjoint==<br />
<br />
From examination of the taxon inconsistency file it would seem that these two processes are not disjoint in principle, though they currently are recorded as being disjoint in GO. <br />
<br />
* According to current thinking, the cellular process term covers processes occurring at the cellular level in a single organism. <br />
* Multi-organism process covers processes that involve more than one organism. <br />
* These two processes are considered disjoint (mutually exclusive), and so cannot have is_a children in common.<br />
<br />
So the question is, where do we put processes ocurring at the cellular level, and including multiple organisms? Examples are 'receptor mediated endocytosis of virus by host' and 'viral transcription'. The process 'receptor mediated endocytosis of virus by host' clearly happens at the cellular level but requires the participation of viral gene products, and so is a cellular multi-organism process. We cannot currently make the term 'cellular multi-organism process' because it would be an is_a child of both multi-organism process and cellular process. This is not allowed, as the two parent terms are disjoint. <br />
<br />
This stucture is not permitted as the two parent terms are disjoint:<br />
<br />
[i]cellular process<br />
---[i]cellular multi-organism process<br />
[i]multi-organism process<br />
---[i]cellular multi-organism process<br />
<br />
Somehow we have to decide whether to place 'receptor mediated endocytosis of virus by host' under cellular process or multi-organism process, but it doesn't make sense to choose, as it is clearly happening at the cellular level, and involves two organisms. <br />
<br />
Currently we have terms that should be descendents of cellular multi-organism process placed as descendents of cellular process, and they have virus annotations. As we start to make more virus annotations, it is inevitable that there will be more terms like this. Such terms are immediately flagged up if a taxon rule is made as follows:<br />
<br />
[Term]<br />
id: GO:0009987<br />
name: cellular process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
(Cellular organisms excludes viruses.)<br />
<br />
It would be helpful to resolve this problem at some point, but this can only be done if the multi-organism process and cellular process are no longer stipulated to be disjoint from one another.<br />
<br />
===Proposal 1===<br />
<br />
I would like to propose that the disjoint relationship between cellular process and multi-organism process be removed, and a child term cellular multi-organism process be created. <br />
<br />
==Proposal 2 - Direct or indirect viral annotations to cellular process should be allowed==<br />
<br />
Following on from the proposal above, if a viral annotation was made to a term such as 'receptor mediated endocytosis of virus by host' and then slimmed up to cellular process, then the annotation would be wrong according to current thinking. (Current GO community understanding is that cellular processes can only be carried out by gene products of cellular organisms, and viruses are not cellular organisms.) <br />
<br />
===Proposal 2===<br />
<br />
I would like to propose that the term cellular process should not be restricted to use only for annotation of gene products of cellular organisms, either in the taxon checking file or in the definition or established understanding of the term. With or without the acceptance of proposal 1, cellular process will still be an ancestor of terms such as 'receptor mediated endocytosis of virus by host' and so it will be as well that annotations should be able to be slimmed up to cellular process without being incorrect.<br />
<br />
==Comments==<br />
<br />
'''Midori''': "I think it would help Val quite a bit with the yeast mating (i.e. conjugation with cellular fusion)."<br><br />
<br><br />
'''Jane''': I think we do need to keep multi-organism processes disjoint with single-organism processes - at the moment cellular processes are always single organism so there isn't a problem. Otherwise I think we'll end up with oddities in slims etc. In the example you give, genes involved in multi-organism processes would end up slimmed to a cellular process parent - that might be very confusing.<br />
<br />
However, to keep them disjoint would lead to this sort of structure:<br />
<br />
single-organism process<br />
---[i] single-organism cellular process<br />
---[i] single-organism multicellular process<br />
multi-organism process<br />
---[i] multi-organism cellular process<br />
---[i] multi-organism multicellular process<br />
multicellular process<br />
---[i] multi-organism multicellular process<br />
---[i] single-organism multicellular process<br />
cellular process<br />
---[i] single-organism cellular process<br />
---[i] multi-organism cellular process<br />
<br />
which I'm not happy with either. I think this warrants more thought. I do see the problem though.<br />
<br />
Thread carries on on the go list:<br />
<br />
'''Re: [Go] disjoint proposal'''<br><br />
'''28/01/2010'''<br />
<br />
==Conclusion==<br />
<br />
''Concludes ''that in fact 'multi-organism process' was really intended to be 'multi-organism process occuring at the cellular, tissue, organ or organism level' whereas 'cellular process' was intended to be 'single organism process occurring at the cellular level'. <br />
<br />
This means that we need to come back to these terms and properly define them and then move the multi-organism processes out of under 'cellular process'.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Are_multi-organism_process_and_cellular_process_disjoint%3F&diff=24428Are multi-organism process and cellular process disjoint?2010-01-28T10:30:28Z<p>Jdeegan: </p>
<hr />
<div>==Proposal 1 - Multi-organism process and cellular process should no longer be disjoint==<br />
<br />
From examination of the taxon inconsistency file it would seem that these two processes are not disjoint in principle, though they currently are recorded as being disjoint in GO. <br />
<br />
* According to current thinking, the cellular process term covers processes occurring at the cellular level in a single organism. <br />
* Multi-organism process covers processes that involve more than one organism. <br />
* These two processes are considered disjoint (mutually exclusive), and so cannot have is_a children in common.<br />
<br />
So the question is, where do we put processes ocurring at the cellular level, and including multiple organisms? Examples are 'receptor mediated endocytosis of virus by host' and 'viral transcription'. The process 'receptor mediated endocytosis of virus by host' clearly happens at the cellular level but requires the participation of viral gene products, and so is a cellular multi-organism process. We cannot currently make the term 'cellular multi-organism process' because it would be an is_a child of both multi-organism process and cellular process. This is not allowed, as the two parent terms are disjoint. <br />
<br />
This stucture is not permitted as the two parent terms are disjoint:<br />
<br />
[i]cellular process<br />
---[i]cellular multi-organism process<br />
[i]multi-organism process<br />
---[i]cellular multi-organism process<br />
<br />
Somehow we have to decide whether to place 'receptor mediated endocytosis of virus by host' under cellular process or multi-organism process, but it doesn't make sense to choose, as it is clearly happening at the cellular level, and involves two organisms. <br />
<br />
Currently we have terms that should be descendents of cellular multi-organism process placed as descendents of cellular process, and they have virus annotations. As we start to make more virus annotations, it is inevitable that there will be more terms like this. Such terms are immediately flagged up if a taxon rule is made as follows:<br />
<br />
[Term]<br />
id: GO:0009987<br />
name: cellular process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
(Cellular organisms excludes viruses.)<br />
<br />
It would be helpful to resolve this problem at some point, but this can only be done if the multi-organism process and cellular process are no longer stipulated to be disjoint from one another.<br />
<br />
===Proposal 1===<br />
<br />
I would like to propose that the disjoint relationship between cellular process and multi-organism process be removed, and a child term cellular multi-organism process be created. <br />
<br />
==Proposal 2 - Direct or indirect viral annotations to cellular process should be allowed==<br />
<br />
Following on from the proposal above, if a viral annotation was made to a term such as 'receptor mediated endocytosis of virus by host' and then slimmed up to cellular process, then the annotation would be wrong according to current thinking. (Current GO community understanding is that cellular processes can only be carried out by gene products of cellular organisms, and viruses are not cellular organisms.) <br />
<br />
===Proposal 2===<br />
<br />
I would like to propose that the term cellular process should not be restricted to use only for annotation of gene products of cellular organisms, either in the taxon checking file or in the definition or established understanding of the term. With or without the acceptance of proposal 1, cellular process will still be an ancestor of terms such as 'receptor mediated endocytosis of virus by host' and so it will be as well that annotations should be able to be slimmed up to cellular process without being incorrect.<br />
<br />
==Comments==<br />
<br />
'''Midori''': "I think it would help Val quite a bit with the yeast mating (i.e. conjugation with cellular fusion)."</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Part_9&diff=24425Taxon-GO Checks and Commentary - Part 92010-01-27T17:11:19Z<p>Jdeegan: </p>
<hr />
<div>January 2010<br />
<br />
Emily Dimmer of GOA has sent this enquiry to Chris:<br />
<br />
<pre><br />
Could I check with you what version of gene association <br />
files you are using in your GO database to query the GO <br />
taxon checks that Jen has generated? I'm very confused <br />
by one of the results from the most recent run -<br />
<br />
protein NCBITaxon:9606 20030904 PINC <br />
GO:0005816 "spindle pole body" only_in NCBITaxon:4751 "Fungi" <br />
:: UniProtKB P23258 TUBG1 GO:0005816 PMID:1904010 <br />
TAS C protein NCBITaxon:9606 20030904 PINC<br />
<br />
This annotation has not been in our gene association file <br />
since the GOA 06/10/2009 human gene association file release.<br />
<br />
It would be ideal if the taxon-checking scripts could be run <br />
over the most recent file releases, so that we can see the <br />
improvements we're making in our annotation sets, and which <br />
annotations we still need to fix.<br />
</pre><br />
<br />
Response:<br />
<br />
This was due to some extra files in the experimental location that Chris was using. Chris will see about moving this all to beta stage so that we have the real files instead of an experimental set. He will also work with Tony Sawford at GOA to get the tests set up in-house with GOA. Tony has already started working on this after a meeting with Jennifer Deegan.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Part_9&diff=24424Taxon-GO Checks and Commentary - Part 92010-01-27T17:11:04Z<p>Jdeegan: </p>
<hr />
<div>Emily Dimmer of GOA has sent this enquiry to Chris:<br />
<br />
<pre><br />
Could I check with you what version of gene association <br />
files you are using in your GO database to query the GO <br />
taxon checks that Jen has generated? I'm very confused <br />
by one of the results from the most recent run -<br />
<br />
protein NCBITaxon:9606 20030904 PINC <br />
GO:0005816 "spindle pole body" only_in NCBITaxon:4751 "Fungi" <br />
:: UniProtKB P23258 TUBG1 GO:0005816 PMID:1904010 <br />
TAS C protein NCBITaxon:9606 20030904 PINC<br />
<br />
This annotation has not been in our gene association file <br />
since the GOA 06/10/2009 human gene association file release.<br />
<br />
It would be ideal if the taxon-checking scripts could be run <br />
over the most recent file releases, so that we can see the <br />
improvements we're making in our annotation sets, and which <br />
annotations we still need to fix.<br />
</pre><br />
<br />
Response:<br />
<br />
This was due to some extra files in the experimental location that Chris was using. Chris will see about moving this all to beta stage so that we have the real files instead of an experimental set. He will also work with Tony Sawford at GOA to get the tests set up in-house with GOA. Tony has already started working on this after a meeting with Jennifer Deegan.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Part_9&diff=24417Taxon-GO Checks and Commentary - Part 92010-01-27T14:37:48Z<p>Jdeegan: </p>
<hr />
<div>Emily Dimmer of GOA has sent this enquiry to Chris:<br />
<br />
<pre><br />
Could I check with you what version of gene association <br />
files you are using in your GO database to query the GO <br />
taxon checks that Jen has generated? I'm very confused <br />
by one of the results from the most recent run -<br />
<br />
protein NCBITaxon:9606 20030904 PINC <br />
GO:0005816 "spindle pole body" only_in NCBITaxon:4751 "Fungi" <br />
:: UniProtKB P23258 TUBG1 GO:0005816 PMID:1904010 <br />
TAS C protein NCBITaxon:9606 20030904 PINC<br />
<br />
This annotation has not been in our gene association file <br />
since the GOA 06/10/2009 human gene association file release.<br />
<br />
It would be ideal if the taxon-checking scripts could be run <br />
over the most recent file releases, so that we can see the <br />
improvements we're making in our annotation sets, and which <br />
annotations we still need to fix.<br />
</pre></div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Part_9&diff=24416Taxon-GO Checks and Commentary - Part 92010-01-27T14:37:22Z<p>Jdeegan: Created page with 'Emily Dimmer of GOA has sent this enquiry to Chris: <pre> Could I check with you what version of gene association files you are using in your GO database to query the GO taxon c…'</p>
<hr />
<div>Emily Dimmer of GOA has sent this enquiry to Chris:<br />
<br />
<pre><br />
Could I check with you what version of gene association files you are using in your GO database to query the GO taxon checks that Jen has generated? I'm very confused by one of the results from the most recent run -<br />
<br />
protein NCBITaxon:9606 20030904 PINC GO:0005816 "spindle pole body" only_in NCBITaxon:4751 "Fungi" :: UniProtKB P23258 TUBG1 GO:0005816 PMID:1904010 TAS C protein NCBITaxon:9606 20030904 PINC<br />
<br />
This annotation has not been in our gene association file since the GOA 06/10/2009 human gene association file release.<br />
<br />
It would be ideal if the taxon-checking scripts could be run over the most recent file releases, so that we can see the improvements we're making in our annotation sets, and which annotations we still need to fix.<br />
</pre></div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon_Main_Page&diff=24415Taxon Main Page2010-01-27T14:36:46Z<p>Jdeegan: </p>
<hr />
<div>[[Manuscript of taxon checking system paper]]<br />
<br />
[[Taxon Trigger File Metrics]]<br />
<br />
[[Proposal 2007]]<br />
<br />
[[Taxon-GO Implementation April 2008 onwards]]<br />
<br />
[[Taxon-GO Implementation April 2009 onwards]]<br />
<br />
[[Taxon-GO Checks and Commentary - Part 1]] - GOA and others<br />
<br />
[[Taxon-GO Checks and Commentary - Part 2]] - FlyBase<br />
<br />
[[Taxon-GO Checks and Commentary - Part 3]] - GOA<br />
<br />
[[Taxon-GO Checks and Commentary - Part 4]] - Viruses<br />
<br />
[[Taxon-GO Checks and Commentary - Part 5]] - MGI, ZFIN and SGD<br />
<br />
[[Taxon-GO Checks and Commentary - Part 6]] - TAIR, RGD and EcoCyc<br />
<br />
[[Taxon-GO Checks and Commentary - Part 7]] - WormBase<br />
<br />
[[Taxon-GO Checks and Commentary - Part 8]] - submission via SourceForge<br />
<br />
[[Taxon-GO Checks and Commentary - Response to GOA - Part 5]]<br />
<br />
[[Taxon-GO Checks and Commentary - Part 9]] - GOA<br />
<br />
[[Resolving redundancies in taxon links]]<br />
<br />
[[Taxon file location in cvs]]<br />
<br />
[[Union term id space]]<br />
<br />
[[To Do List - Taxon checks]]<br />
<br />
[[Are Multi-organism process and cellular process disjoint?]]<br />
<br />
<br />
[[Taxon Editing Workflow]] up until 12th June 2009<br />
<br />
[[Taxon Editing Workflow after 12th June 2009]]<br />
<br />
[[GAF_Taxonomy_Reasoning]]<br />
<br />
[[Category:Taxon]]</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Response_to_GOA_-_Part_5&diff=24411Taxon-GO Checks and Commentary - Response to GOA - Part 52010-01-27T14:34:46Z<p>Jdeegan: </p>
<hr />
<div> Line 7: TAXON RULE INCORRECT THIS TERM SHOULD INCLUDE VIRUSES GO:0019064 "viral envelope fusion with host membrane" only_in NCBITaxon:131567 "cellular organisms" :: Swiss-Prot P36334 S GO:0019064 PMID:11162792 TAS P protein NCBITaxon:31631 20030508 UniProtKB <br />
<br />
'''Q/''' Should viral envelope fusion with host membrane really be an is_a to cellular process? Viral gene products can be annotated to this. <br />
<br />
Line 19: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009775 "photosynthetic electron transport in cytochrome b6/f" only_in ID:0000000 "Viridiplantae or Bacteria" :: Swiss-Prot P31480 petB GO:0009775 PMID:12837550 NAS P protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' New union term made and rule corrected.<br />
<br />
Line 21: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot P83687 PSBP GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' New union term made for Viridiplantae and Euglenozoa.<br />
<br />
Line 22: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot Q8GZR2 petA GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
Line 23: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot P83688 P83688 GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 25: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009512 "cytochrome b6f complex" only_in JD:0000002 "Viridiplantae or Cyanobacteria" :: Swiss-Prot Q84TU6 petD GO:0009512 PMID:12837550 IDA C protein NCBITaxon:3039 20040507 UniProtKB <br />
<br />
'''A/''' Changed to Viridiplantae or bacteria or Euglenozoa.<br />
<br />
Line 26: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009512 "cytochrome b6f complex" only_in JD:0000002 "Viridiplantae or Cyanobacteria" :: Swiss-Prot P31480 petB GO:0009512 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 36: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q54714 cpcB GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB <br />
<br />
'''A/''' This rule is not present. Perhaps it was previously corrected. <br />
<br />
Line 37: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q54715 cpcA GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 38: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q01951 apcA GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 49: TAXON RULE INCORRECT: GO:0006260 "DNA replication" only_in NCBITaxon:131567 "cellular organisms" :: TrEMBL O00529 O00529 GO:0006260 GO_REF:0000029 NAS P protein NCBITaxon:333760 20021106 UniProtKB <br />
<br />
'''A/''' This is a problem in the graph. We need generic and cellular versions of DNA replication. <br />
<br />
Line 52: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9XHP1 Q9XHP1 GO:0045735 PMID:10606554 NAS F protein NCBITaxon:4182 20051104 UniProtKB <br />
<br />
'''A/''' This rule appears to be gone already. <br />
<br />
Line 53: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9SPL3 AMP2-3 GO:0045735 PMID:10571855 NAS F protein NCBITaxon:60698 20060904 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 54: TAXON RULE INCORRECT. (annotation to a major plant storage protein)GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9XHP0 Q9XHP0 GO:0045735 PMID:10606554 NAS F protein NCBITaxon:4182 20051104 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 55: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q39649 Q39649 GO:0045735 PMID:8275099 TAS F protein NCBITaxon:3661 20050516 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 82: TAXON RULE INCORRECT GO:0008274 "gamma-tubulin ring complex" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot Q95K09 TUBGCP5 GO:0008274 PMID:11694571 ISS UniProtKB:Q96RT8 C protein NCBITaxon:9541 20041006 UniProtKB <br />
<br />
'''A/''' Rule deleted. <br />
<br />
Line 84: TAXON RULE INCORRECT GO:0008274 "gamma-tubulin ring complex" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot Q9GKK8 BRCA1 GO:0008274 PMID:12214252 NAS C protein NCBITaxon:9598 20021218 UniProtKB <br />
<br />
'''A/''' Rule deleted. <br />
<br />
Line 97: TAXON RULE INCORRECT.GO:0042475 "odontogenesis of dentine-containing tooth" only_in NCBITaxon:33317 "Protostomia" :: MGI MGI:104659 Dll1 GO:0042475 MGI:MGI:1327472|PMID:9882480 NAS P gene NCBITaxon:10090 20021218 UniProtKB<br />
<br />
'''A/''' Bumped this up to Chordata from the current position under Vertebrate to see if that solves the problem. <br />
<br />
Line 98: TAXON RULE INCORRECT.GO:0042476 "odontogenesis" only_in NCBITaxon:33317 "Protostomia" :: MGI MGI:1914505 Zfp422 GO:0042476 MGI:MGI:2449683|PMID:12489153 NAS P gene NCBITaxon:10090 20040226 UniProtKB <br />
<br />
'''A/''' Deleted rule<br />
<br />
Line 99: TAXON RULE INCORRECT.GO:0042476 "odontogenesis" only_in NCBITaxon:33317 "Protostomia" :: RGD 620229 Zfp422 GO:0042476 RGD:14706453 NAS P gene NCBITaxon:10116 20040226 UniProtKB <br />
<br />
'''A/''' Deleted rule.<br />
<br />
==Ontology Corrections==<br />
<br />
<br />
===DNA Replication===<br />
<br />
Line 49: TAXON RULE INCORRECT: GO:0006260 "DNA replication" only_in NCBITaxon:131567 "cellular organisms" :: TrEMBL O00529 O00529 GO:0006260 GO_REF:0000029 NAS P protein NCBITaxon:333760 20021106 UniProtKB <br />
<br />
'''A/''' This is a problem in the graph. We need generic and cellular versions of DNA replication. <br />
<br />
Terms created:<br />
<br />
<pre><br />
> id: GO:0055132<br />
> name: cellular DNA metabolic process<br />
<br />
> id: GO:0055133<br />
> name: cellular DNA replication<br />
<br />
> id: GO:0055134<br />
> name: cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process<br />
<br />
</pre><br />
<br />
<br />
===Viral annotations to non-cellular terms with cellular ancestors===<br />
<br />
Line 7: TAXON RULE INCORRECT THIS TERM SHOULD INCLUDE VIRUSES GO:0019064 "viral envelope fusion with host membrane" only_in NCBITaxon:131567 "cellular organisms" :: Swiss-Prot P36334 S GO:0019064 PMID:11162792 TAS P protein NCBITaxon:31631 20030508 UniProtKB <br />
<br />
'''Q/''' Should viral envelope fusion with host membrane really be an is_a to cellular process? Viral gene products can be annotated to this.<br />
<br />
- Removed the rule that locomotion (GO:0040011) is only in cellular organisms. <br />
<br />
- Removed link from membrane organization (GO:0016044) to cellular process.<br />
<br />
===Viruses and response to stimulus===<br />
<br />
GO:0052085 "negative regulation by symbiont of host T-cell mediated immune<br />
response" only_in NCBITaxon:131567 "cellular organisms"<br />
<br />
From checking with Jane it appears that a symbiont can also be a virus, so<br />
this taxon rule should be removed<br />
<br />
A/<br />
<br />
I have removed this rule:<br />
<br />
<pre><br />
[Term]<br />
id: GO:0050896<br />
name: response to stimulus<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
</pre><br />
<br />
This does not hold true as viruses also respond to the stimuli produced by their hosts.<br />
<br />
For similar reasons I have removed these links:<br />
<br />
[Term]<br />
id: GO:0051179<br />
name: localization<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
[Term]<br />
id: GO:0032502<br />
name: developmental process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
==Cellular process only_in_taxon cellular organisms?==<br />
<br />
id: GO:0009987<br />
name: cellular process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
I have removed this rule for the reasons stated in my [http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F proposal].</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Response_to_GOA_-_Part_5&diff=24410Taxon-GO Checks and Commentary - Response to GOA - Part 52010-01-27T14:34:30Z<p>Jdeegan: </p>
<hr />
<div> Line 7: TAXON RULE INCORRECT THIS TERM SHOULD INCLUDE VIRUSES GO:0019064 "viral envelope fusion with host membrane" only_in NCBITaxon:131567 "cellular organisms" :: Swiss-Prot P36334 S GO:0019064 PMID:11162792 TAS P protein NCBITaxon:31631 20030508 UniProtKB <br />
<br />
'''Q/''' Should viral envelope fusion with host membrane really be an is_a to cellular process? Viral gene products can be annotated to this. <br />
<br />
Line 19: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009775 "photosynthetic electron transport in cytochrome b6/f" only_in ID:0000000 "Viridiplantae or Bacteria" :: Swiss-Prot P31480 petB GO:0009775 PMID:12837550 NAS P protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' New union term made and rule corrected.<br />
<br />
Line 21: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot P83687 PSBP GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' New union term made for Viridiplantae and Euglenozoa.<br />
<br />
Line 22: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot Q8GZR2 petA GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
Line 23: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot P83688 P83688 GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 25: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009512 "cytochrome b6f complex" only_in JD:0000002 "Viridiplantae or Cyanobacteria" :: Swiss-Prot Q84TU6 petD GO:0009512 PMID:12837550 IDA C protein NCBITaxon:3039 20040507 UniProtKB <br />
<br />
'''A/''' Changed to Viridiplantae or bacteria or Euglenozoa.<br />
<br />
Line 26: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009512 "cytochrome b6f complex" only_in JD:0000002 "Viridiplantae or Cyanobacteria" :: Swiss-Prot P31480 petB GO:0009512 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 36: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q54714 cpcB GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB <br />
<br />
'''A/''' This rule is not present. Perhaps it was previously corrected. <br />
<br />
Line 37: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q54715 cpcA GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 38: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q01951 apcA GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 49: TAXON RULE INCORRECT: GO:0006260 "DNA replication" only_in NCBITaxon:131567 "cellular organisms" :: TrEMBL O00529 O00529 GO:0006260 GO_REF:0000029 NAS P protein NCBITaxon:333760 20021106 UniProtKB <br />
<br />
'''A/''' This is a problem in the graph. We need generic and cellular versions of DNA replication. <br />
<br />
Line 52: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9XHP1 Q9XHP1 GO:0045735 PMID:10606554 NAS F protein NCBITaxon:4182 20051104 UniProtKB <br />
<br />
'''A/''' This rule appears to be gone already. <br />
<br />
Line 53: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9SPL3 AMP2-3 GO:0045735 PMID:10571855 NAS F protein NCBITaxon:60698 20060904 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 54: TAXON RULE INCORRECT. (annotation to a major plant storage protein)GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9XHP0 Q9XHP0 GO:0045735 PMID:10606554 NAS F protein NCBITaxon:4182 20051104 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 55: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q39649 Q39649 GO:0045735 PMID:8275099 TAS F protein NCBITaxon:3661 20050516 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 82: TAXON RULE INCORRECT GO:0008274 "gamma-tubulin ring complex" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot Q95K09 TUBGCP5 GO:0008274 PMID:11694571 ISS UniProtKB:Q96RT8 C protein NCBITaxon:9541 20041006 UniProtKB <br />
<br />
'''A/''' Rule deleted. <br />
<br />
Line 84: TAXON RULE INCORRECT GO:0008274 "gamma-tubulin ring complex" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot Q9GKK8 BRCA1 GO:0008274 PMID:12214252 NAS C protein NCBITaxon:9598 20021218 UniProtKB <br />
<br />
'''A/''' Rule deleted. <br />
<br />
Line 97: TAXON RULE INCORRECT.GO:0042475 "odontogenesis of dentine-containing tooth" only_in NCBITaxon:33317 "Protostomia" :: MGI MGI:104659 Dll1 GO:0042475 MGI:MGI:1327472|PMID:9882480 NAS P gene NCBITaxon:10090 20021218 UniProtKB<br />
<br />
'''A/''' Bumped this up to Chordata from the current position under Vertebrate to see if that solves the problem. <br />
<br />
Line 98: TAXON RULE INCORRECT.GO:0042476 "odontogenesis" only_in NCBITaxon:33317 "Protostomia" :: MGI MGI:1914505 Zfp422 GO:0042476 MGI:MGI:2449683|PMID:12489153 NAS P gene NCBITaxon:10090 20040226 UniProtKB <br />
<br />
'''A/''' Deleted rule<br />
<br />
Line 99: TAXON RULE INCORRECT.GO:0042476 "odontogenesis" only_in NCBITaxon:33317 "Protostomia" :: RGD 620229 Zfp422 GO:0042476 RGD:14706453 NAS P gene NCBITaxon:10116 20040226 UniProtKB <br />
<br />
'''A/''' Deleted rule.<br />
<br />
==Ontology Corrections==<br />
<br />
<br />
===DNA Replication===<br />
<br />
Line 49: TAXON RULE INCORRECT: GO:0006260 "DNA replication" only_in NCBITaxon:131567 "cellular organisms" :: TrEMBL O00529 O00529 GO:0006260 GO_REF:0000029 NAS P protein NCBITaxon:333760 20021106 UniProtKB <br />
<br />
'''A/''' This is a problem in the graph. We need generic and cellular versions of DNA replication. <br />
<br />
Terms created:<br />
<br />
<pre><br />
> id: GO:0055132<br />
> name: cellular DNA metabolic process<br />
<br />
> id: GO:0055133<br />
> name: cellular DNA replication<br />
<br />
> id: GO:0055134<br />
> name: cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process<br />
<br />
</pre><br />
<br />
<br />
===Viral annotations to non-cellular terms with cellular ancestors===<br />
<br />
Line 7: TAXON RULE INCORRECT THIS TERM SHOULD INCLUDE VIRUSES GO:0019064 "viral envelope fusion with host membrane" only_in NCBITaxon:131567 "cellular organisms" :: Swiss-Prot P36334 S GO:0019064 PMID:11162792 TAS P protein NCBITaxon:31631 20030508 UniProtKB <br />
<br />
'''Q/''' Should viral envelope fusion with host membrane really be an is_a to cellular process? Viral gene products can be annotated to this.<br />
<br />
- Removed the rule that locomotion (GO:0040011) is only in cellular organisms. <br />
<br />
- Removed link from membrane organization (GO:0016044) to cellular process.<br />
<br />
===Viruses and response to stimulus===<br />
<br />
GO:0052085 "negative regulation by symbiont of host T-cell mediated immune<br />
response" only_in NCBITaxon:131567 "cellular organisms"<br />
<br />
From checking with Jane it appears that a symbiont can also be a virus, so<br />
this taxon rule should be removed<br />
<br />
A/<br />
<br />
I have removed this rule:<br />
<br />
<pre><br />
[Term]<br />
id: GO:0050896<br />
name: response to stimulus<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
</pre><br />
<br />
This does not hold true as viruses also respond to the stimuli produced by their hosts.<br />
<br />
For similar reasons I have removed these links:<br />
<br />
[Term]<br />
id: GO:0051179<br />
name: localization<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
[Term]<br />
id: GO:0032502<br />
name: developmental process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
==Cellular process only_in_taxon cellular organisms?==<br />
<br />
id: GO:0009987<br />
name: cellular process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
I have removed this rule for the reasons stated in my [http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F proposal].</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Response_to_GOA_-_Part_5&diff=24408Taxon-GO Checks and Commentary - Response to GOA - Part 52010-01-27T14:33:08Z<p>Jdeegan: </p>
<hr />
<div> Line 7: TAXON RULE INCORRECT THIS TERM SHOULD INCLUDE VIRUSES GO:0019064 "viral envelope fusion with host membrane" only_in NCBITaxon:131567 "cellular organisms" :: Swiss-Prot P36334 S GO:0019064 PMID:11162792 TAS P protein NCBITaxon:31631 20030508 UniProtKB <br />
<br />
'''Q/''' Should viral envelope fusion with host membrane really be an is_a to cellular process? Viral gene products can be annotated to this. <br />
<br />
Line 19: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009775 "photosynthetic electron transport in cytochrome b6/f" only_in ID:0000000 "Viridiplantae or Bacteria" :: Swiss-Prot P31480 petB GO:0009775 PMID:12837550 NAS P protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' New union term made and rule corrected.<br />
<br />
Line 21: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot P83687 PSBP GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' New union term made for Viridiplantae and Euglenozoa.<br />
<br />
Line 22: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot Q8GZR2 petA GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
Line 23: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot P83688 P83688 GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 25: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009512 "cytochrome b6f complex" only_in JD:0000002 "Viridiplantae or Cyanobacteria" :: Swiss-Prot Q84TU6 petD GO:0009512 PMID:12837550 IDA C protein NCBITaxon:3039 20040507 UniProtKB <br />
<br />
'''A/''' Changed to Viridiplantae or bacteria or Euglenozoa.<br />
<br />
Line 26: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009512 "cytochrome b6f complex" only_in JD:0000002 "Viridiplantae or Cyanobacteria" :: Swiss-Prot P31480 petB GO:0009512 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 36: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q54714 cpcB GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB <br />
<br />
'''A/''' This rule is not present. Perhaps it was previously corrected. <br />
<br />
Line 37: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q54715 cpcA GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 38: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q01951 apcA GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 49: TAXON RULE INCORRECT: GO:0006260 "DNA replication" only_in NCBITaxon:131567 "cellular organisms" :: TrEMBL O00529 O00529 GO:0006260 GO_REF:0000029 NAS P protein NCBITaxon:333760 20021106 UniProtKB <br />
<br />
'''A/''' This is a problem in the graph. We need generic and cellular versions of DNA replication. <br />
<br />
Line 52: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9XHP1 Q9XHP1 GO:0045735 PMID:10606554 NAS F protein NCBITaxon:4182 20051104 UniProtKB <br />
<br />
'''A/''' This rule appears to be gone already. <br />
<br />
Line 53: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9SPL3 AMP2-3 GO:0045735 PMID:10571855 NAS F protein NCBITaxon:60698 20060904 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 54: TAXON RULE INCORRECT. (annotation to a major plant storage protein)GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9XHP0 Q9XHP0 GO:0045735 PMID:10606554 NAS F protein NCBITaxon:4182 20051104 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 55: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q39649 Q39649 GO:0045735 PMID:8275099 TAS F protein NCBITaxon:3661 20050516 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 82: TAXON RULE INCORRECT GO:0008274 "gamma-tubulin ring complex" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot Q95K09 TUBGCP5 GO:0008274 PMID:11694571 ISS UniProtKB:Q96RT8 C protein NCBITaxon:9541 20041006 UniProtKB <br />
<br />
'''A/''' Rule deleted. <br />
<br />
Line 84: TAXON RULE INCORRECT GO:0008274 "gamma-tubulin ring complex" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot Q9GKK8 BRCA1 GO:0008274 PMID:12214252 NAS C protein NCBITaxon:9598 20021218 UniProtKB <br />
<br />
'''A/''' Rule deleted. <br />
<br />
Line 97: TAXON RULE INCORRECT.GO:0042475 "odontogenesis of dentine-containing tooth" only_in NCBITaxon:33317 "Protostomia" :: MGI MGI:104659 Dll1 GO:0042475 MGI:MGI:1327472|PMID:9882480 NAS P gene NCBITaxon:10090 20021218 UniProtKB<br />
<br />
'''A/''' Bumped this up to Chordata from the current position under Vertebrate to see if that solves the problem. <br />
<br />
Line 98: TAXON RULE INCORRECT.GO:0042476 "odontogenesis" only_in NCBITaxon:33317 "Protostomia" :: MGI MGI:1914505 Zfp422 GO:0042476 MGI:MGI:2449683|PMID:12489153 NAS P gene NCBITaxon:10090 20040226 UniProtKB <br />
<br />
'''A/''' Deleted rule<br />
<br />
Line 99: TAXON RULE INCORRECT.GO:0042476 "odontogenesis" only_in NCBITaxon:33317 "Protostomia" :: RGD 620229 Zfp422 GO:0042476 RGD:14706453 NAS P gene NCBITaxon:10116 20040226 UniProtKB <br />
<br />
'''A/''' Deleted rule.<br />
<br />
==Ontology Corrections==<br />
<br />
<br />
===DNA Replication===<br />
<br />
Line 49: TAXON RULE INCORRECT: GO:0006260 "DNA replication" only_in NCBITaxon:131567 "cellular organisms" :: TrEMBL O00529 O00529 GO:0006260 GO_REF:0000029 NAS P protein NCBITaxon:333760 20021106 UniProtKB <br />
<br />
'''A/''' This is a problem in the graph. We need generic and cellular versions of DNA replication. <br />
<br />
Terms created:<br />
<br />
<pre><br />
> id: GO:0055132<br />
> name: cellular DNA metabolic process<br />
<br />
> id: GO:0055133<br />
> name: cellular DNA replication<br />
<br />
> id: GO:0055134<br />
> name: cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process<br />
<br />
</pre><br />
<br />
<br />
===Viral annotations to non-cellular terms with cellular ancestors===<br />
<br />
Line 7: TAXON RULE INCORRECT THIS TERM SHOULD INCLUDE VIRUSES GO:0019064 "viral envelope fusion with host membrane" only_in NCBITaxon:131567 "cellular organisms" :: Swiss-Prot P36334 S GO:0019064 PMID:11162792 TAS P protein NCBITaxon:31631 20030508 UniProtKB <br />
<br />
'''Q/''' Should viral envelope fusion with host membrane really be an is_a to cellular process? Viral gene products can be annotated to this.<br />
<br />
- Removed the rule that locomotion (GO:0040011) is only in cellular organisms. <br />
<br />
- Removed link from membrane organization (GO:0016044) to cellular process.<br />
<br />
===Viruses and response to stimulus===<br />
<br />
GO:0052085 "negative regulation by symbiont of host T-cell mediated immune<br />
response" only_in NCBITaxon:131567 "cellular organisms"<br />
<br />
From checking with Jane it appears that a symbiont can also be a virus, so<br />
this taxon rule should be removed<br />
<br />
A/<br />
<br />
I have removed this rule:<br />
<br />
<pre><br />
[Term]<br />
id: GO:0050896<br />
name: response to stimulus<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
</pre><br />
<br />
This does not hold true as viruses also respond to the stimuli produced by their hosts.<br />
<br />
For similar reasons I have removed these links:<br />
<br />
[Term]<br />
id: GO:0051179<br />
name: localization<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
[Term]<br />
id: GO:0032502<br />
name: developmental process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
==Cellular process only_in_taxon cellular organisms?==<br />
<br />
id: GO:0009987<br />
name: cellular process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
I have removed this rule for the reasons stated in my [proposal http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F].</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Taxon-GO_Checks_and_Commentary_-_Response_to_GOA_-_Part_5&diff=24407Taxon-GO Checks and Commentary - Response to GOA - Part 52010-01-27T14:32:48Z<p>Jdeegan: </p>
<hr />
<div> Line 7: TAXON RULE INCORRECT THIS TERM SHOULD INCLUDE VIRUSES GO:0019064 "viral envelope fusion with host membrane" only_in NCBITaxon:131567 "cellular organisms" :: Swiss-Prot P36334 S GO:0019064 PMID:11162792 TAS P protein NCBITaxon:31631 20030508 UniProtKB <br />
<br />
'''Q/''' Should viral envelope fusion with host membrane really be an is_a to cellular process? Viral gene products can be annotated to this. <br />
<br />
Line 19: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009775 "photosynthetic electron transport in cytochrome b6/f" only_in ID:0000000 "Viridiplantae or Bacteria" :: Swiss-Prot P31480 petB GO:0009775 PMID:12837550 NAS P protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' New union term made and rule corrected.<br />
<br />
Line 21: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot P83687 PSBP GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' New union term made for Viridiplantae and Euglenozoa.<br />
<br />
Line 22: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot Q8GZR2 petA GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
Line 23: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS GO:0009507 "chloroplast" only_in NCBITaxon:33090 "Viridiplantae" :: Swiss-Prot P83688 P83688 GO:0009507 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 25: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009512 "cytochrome b6f complex" only_in JD:0000002 "Viridiplantae or Cyanobacteria" :: Swiss-Prot Q84TU6 petD GO:0009512 PMID:12837550 IDA C protein NCBITaxon:3039 20040507 UniProtKB <br />
<br />
'''A/''' Changed to Viridiplantae or bacteria or Euglenozoa.<br />
<br />
Line 26: TAXON RULE INCORRECT EUGELA CONTAIN CHLOROPLASTS AND cytochrome b6f complex GO:0009512 "cytochrome b6f complex" only_in JD:0000002 "Viridiplantae or Cyanobacteria" :: Swiss-Prot P31480 petB GO:0009512 PMID:12837550 IDA C protein NCBITaxon:3039 20031120 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 36: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q54714 cpcB GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB <br />
<br />
'''A/''' This rule is not present. Perhaps it was previously corrected. <br />
<br />
Line 37: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q54715 cpcA GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 38: TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phycobilisome" only_in NCBITaxon:2759 "Eukaryota" :: Swiss-Prot Q01951 apcA GO:0030089 PMID:14730074 IDA C protein NCBITaxon:1148 20050613 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 49: TAXON RULE INCORRECT: GO:0006260 "DNA replication" only_in NCBITaxon:131567 "cellular organisms" :: TrEMBL O00529 O00529 GO:0006260 GO_REF:0000029 NAS P protein NCBITaxon:333760 20021106 UniProtKB <br />
<br />
'''A/''' This is a problem in the graph. We need generic and cellular versions of DNA replication. <br />
<br />
Line 52: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9XHP1 Q9XHP1 GO:0045735 PMID:10606554 NAS F protein NCBITaxon:4182 20051104 UniProtKB <br />
<br />
'''A/''' This rule appears to be gone already. <br />
<br />
Line 53: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9SPL3 AMP2-3 GO:0045735 PMID:10571855 NAS F protein NCBITaxon:60698 20060904 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 54: TAXON RULE INCORRECT. (annotation to a major plant storage protein)GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q9XHP0 Q9XHP0 GO:0045735 PMID:10606554 NAS F protein NCBITaxon:4182 20051104 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 55: TAXON RULE INCORRECT. (annotation to a major plant storage protein) GO:0045735 "nutrient reservoir activity" only_in NCBITaxon:88770 "Panarthropoda" :: Swiss-Prot Q39649 Q39649 GO:0045735 PMID:8275099 TAS F protein NCBITaxon:3661 20050516 UniProtKB <br />
<br />
'''A/''' As above.<br />
<br />
Line 82: TAXON RULE INCORRECT GO:0008274 "gamma-tubulin ring complex" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot Q95K09 TUBGCP5 GO:0008274 PMID:11694571 ISS UniProtKB:Q96RT8 C protein NCBITaxon:9541 20041006 UniProtKB <br />
<br />
'''A/''' Rule deleted. <br />
<br />
Line 84: TAXON RULE INCORRECT GO:0008274 "gamma-tubulin ring complex" only_in NCBITaxon:4751 "Fungi" :: Swiss-Prot Q9GKK8 BRCA1 GO:0008274 PMID:12214252 NAS C protein NCBITaxon:9598 20021218 UniProtKB <br />
<br />
'''A/''' Rule deleted. <br />
<br />
Line 97: TAXON RULE INCORRECT.GO:0042475 "odontogenesis of dentine-containing tooth" only_in NCBITaxon:33317 "Protostomia" :: MGI MGI:104659 Dll1 GO:0042475 MGI:MGI:1327472|PMID:9882480 NAS P gene NCBITaxon:10090 20021218 UniProtKB<br />
<br />
'''A/''' Bumped this up to Chordata from the current position under Vertebrate to see if that solves the problem. <br />
<br />
Line 98: TAXON RULE INCORRECT.GO:0042476 "odontogenesis" only_in NCBITaxon:33317 "Protostomia" :: MGI MGI:1914505 Zfp422 GO:0042476 MGI:MGI:2449683|PMID:12489153 NAS P gene NCBITaxon:10090 20040226 UniProtKB <br />
<br />
'''A/''' Deleted rule<br />
<br />
Line 99: TAXON RULE INCORRECT.GO:0042476 "odontogenesis" only_in NCBITaxon:33317 "Protostomia" :: RGD 620229 Zfp422 GO:0042476 RGD:14706453 NAS P gene NCBITaxon:10116 20040226 UniProtKB <br />
<br />
'''A/''' Deleted rule.<br />
<br />
==Ontology Corrections==<br />
<br />
<br />
===DNA Replication===<br />
<br />
Line 49: TAXON RULE INCORRECT: GO:0006260 "DNA replication" only_in NCBITaxon:131567 "cellular organisms" :: TrEMBL O00529 O00529 GO:0006260 GO_REF:0000029 NAS P protein NCBITaxon:333760 20021106 UniProtKB <br />
<br />
'''A/''' This is a problem in the graph. We need generic and cellular versions of DNA replication. <br />
<br />
Terms created:<br />
<br />
<pre><br />
> id: GO:0055132<br />
> name: cellular DNA metabolic process<br />
<br />
> id: GO:0055133<br />
> name: cellular DNA replication<br />
<br />
> id: GO:0055134<br />
> name: cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process<br />
<br />
</pre><br />
<br />
<br />
===Viral annotations to non-cellular terms with cellular ancestors===<br />
<br />
Line 7: TAXON RULE INCORRECT THIS TERM SHOULD INCLUDE VIRUSES GO:0019064 "viral envelope fusion with host membrane" only_in NCBITaxon:131567 "cellular organisms" :: Swiss-Prot P36334 S GO:0019064 PMID:11162792 TAS P protein NCBITaxon:31631 20030508 UniProtKB <br />
<br />
'''Q/''' Should viral envelope fusion with host membrane really be an is_a to cellular process? Viral gene products can be annotated to this.<br />
<br />
- Removed the rule that locomotion (GO:0040011) is only in cellular organisms. <br />
<br />
- Removed link from membrane organization (GO:0016044) to cellular process.<br />
<br />
===Viruses and response to stimulus===<br />
<br />
GO:0052085 "negative regulation by symbiont of host T-cell mediated immune<br />
response" only_in NCBITaxon:131567 "cellular organisms"<br />
<br />
From checking with Jane it appears that a symbiont can also be a virus, so<br />
this taxon rule should be removed<br />
<br />
A/<br />
<br />
I have removed this rule:<br />
<br />
<pre><br />
[Term]<br />
id: GO:0050896<br />
name: response to stimulus<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
</pre><br />
<br />
This does not hold true as viruses also respond to the stimuli produced by their hosts.<br />
<br />
For similar reasons I have removed these links:<br />
<br />
[Term]<br />
id: GO:0051179<br />
name: localization<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
[Term]<br />
id: GO:0032502<br />
name: developmental process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
==Cellular process only_in_taxon cellular organisms?==<br />
<br />
id: GO:0009987<br />
name: cellular process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
I have removed this rule for the reasons stated in my [[proposal http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F]].</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Are_multi-organism_process_and_cellular_process_disjoint%3F&diff=24406Are multi-organism process and cellular process disjoint?2010-01-27T14:25:33Z<p>Jdeegan: </p>
<hr />
<div>==Proposal 1 - Multi-organism process and cellular process should no longer be disjoint==<br />
<br />
From examination of the taxon inconsistency file it would seem that these two processes are not disjoint in principle, though they currently are recorded as being disjoint in GO. <br />
<br />
* According to current thinking, the cellular process term covers processes occurring at the cellular level in a single organism. <br />
* Multi-organism process covers processes that involve more than one organism. <br />
* These two processes are considered disjoint (mutually exclusive), and so cannot have is_a children in common.<br />
<br />
So the question is, where do we put processes ocurring at the cellular level, and including multiple organisms? Examples are 'receptor mediated endocytosis of virus by host' and 'viral transcription'. The process 'receptor mediated endocytosis of virus by host' clearly happens at the cellular level but requires the participation of viral gene products, and so is a cellular multi-organism process. We cannot currently make the term 'cellular multi-organism process' because it would be an is_a child of both multi-organism process and cellular process. This is not allowed, as the two parent terms are disjoint. <br />
<br />
This stucture is not permitted as the two parent terms are disjoint:<br />
<br />
[i]cellular process<br />
---[i]cellular multi-organism process<br />
[i]multi-organism process<br />
---[i]cellular multi-organism process<br />
<br />
Somehow we have to decide whether to place 'receptor mediated endocytosis of virus by host' under cellular process or multi-organism process, but it doesn't make sense to choose, as it is clearly happening at the cellular level, and involves two organisms. <br />
<br />
Currently we have terms that should be descendents of cellular multi-organism process placed as descendents of cellular process, and they have virus annotations. As we start to make more virus annotations, it is inevitable that there will be more terms like this. Such terms are immediately flagged up if a taxon rule is made as follows:<br />
<br />
[Term]<br />
id: GO:0009987<br />
name: cellular process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
(Cellular organisms excludes viruses.)<br />
<br />
It would be helpful to resolve this problem at some point, but this can only be done if the multi-organism process and cellular process are no longer stipulated to be disjoint from one another.<br />
<br />
===Proposal 1===<br />
<br />
I would like to propose that the disjoint relationship between cellular process and multi-organism process be removed, and a child term cellular multi-organism process be created. <br />
<br />
==Proposal 2 - Direct or indirect viral annotations to cellular process should be allowed==<br />
<br />
Following on from the proposal above, if a viral annotation was made to a term such as 'receptor mediated endocytosis of virus by host' and then slimmed up to cellular process, then the annotation would be wrong according to current thinking. (Current GO community understanding is that cellular processes can only be carried out by gene products of cellular organisms, and viruses are not cellular organisms.) <br />
<br />
===Proposal 2===<br />
<br />
I would like to propose that the term cellular process should not be restricted to use only for annotation of gene products of cellular organisms, either in the taxon checking file or in the definition or established understanding of the term. With or without the acceptance of proposal 1, cellular process will still be an ancestor of terms such as 'receptor mediated endocytosis of virus by host' and so it will be as well that annotations should be able to be slimmed up to cellular process without being incorrect.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Are_multi-organism_process_and_cellular_process_disjoint%3F&diff=24405Are multi-organism process and cellular process disjoint?2010-01-27T14:25:17Z<p>Jdeegan: </p>
<hr />
<div>Two proposals:<br />
<br />
==Proposal 1 - Multi-organism process and cellular process should no longer be disjoint==<br />
<br />
From examination of the taxon inconsistency file it would seem that these two processes are not disjoint in principle, though they currently are recorded as being disjoint in GO. <br />
<br />
* According to current thinking, the cellular process term covers processes occurring at the cellular level in a single organism. <br />
* Multi-organism process covers processes that involve more than one organism. <br />
* These two processes are considered disjoint (mutually exclusive), and so cannot have is_a children in common.<br />
<br />
So the question is, where do we put processes ocurring at the cellular level, and including multiple organisms? Examples are 'receptor mediated endocytosis of virus by host' and 'viral transcription'. The process 'receptor mediated endocytosis of virus by host' clearly happens at the cellular level but requires the participation of viral gene products, and so is a cellular multi-organism process. We cannot currently make the term 'cellular multi-organism process' because it would be an is_a child of both multi-organism process and cellular process. This is not allowed, as the two parent terms are disjoint. <br />
<br />
This stucture is not permitted as the two parent terms are disjoint:<br />
<br />
[i]cellular process<br />
---[i]cellular multi-organism process<br />
[i]multi-organism process<br />
---[i]cellular multi-organism process<br />
<br />
Somehow we have to decide whether to place 'receptor mediated endocytosis of virus by host' under cellular process or multi-organism process, but it doesn't make sense to choose, as it is clearly happening at the cellular level, and involves two organisms. <br />
<br />
Currently we have terms that should be descendents of cellular multi-organism process placed as descendents of cellular process, and they have virus annotations. As we start to make more virus annotations, it is inevitable that there will be more terms like this. Such terms are immediately flagged up if a taxon rule is made as follows:<br />
<br />
[Term]<br />
id: GO:0009987<br />
name: cellular process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
<br />
(Cellular organisms excludes viruses.)<br />
<br />
It would be helpful to resolve this problem at some point, but this can only be done if the multi-organism process and cellular process are no longer stipulated to be disjoint from one another.<br />
<br />
===Proposal 1===<br />
<br />
I would like to propose that the disjoint relationship between cellular process and multi-organism process be removed, and a child term cellular multi-organism process be created. <br />
<br />
==Proposal 2 - Direct or indirect viral annotations to cellular process should be allowed==<br />
<br />
Following on from the proposal above, if a viral annotation was made to a term such as 'receptor mediated endocytosis of virus by host' and then slimmed up to cellular process, then the annotation would be wrong according to current thinking. (Current GO community understanding is that cellular processes can only be carried out by gene products of cellular organisms, and viruses are not cellular organisms.) <br />
<br />
===Proposal 2===<br />
<br />
I would like to propose that the term cellular process should not be restricted to use only for annotation of gene products of cellular organisms, either in the taxon checking file or in the definition or established understanding of the term. With or without the acceptance of proposal 1, cellular process will still be an ancestor of terms such as 'receptor mediated endocytosis of virus by host' and so it will be as well that annotations should be able to be slimmed up to cellular process without being incorrect.</div>Jdeeganhttps://wiki.geneontology.org/index.php?title=Are_multi-organism_process_and_cellular_process_disjoint%3F&diff=24404Are multi-organism process and cellular process disjoint?2010-01-27T14:10:28Z<p>Jdeegan: </p>
<hr />
<div>Two proposals:<br />
<br />
==Multi-organism process and cellular process should no longer be disjoint==<br />
<br />
From examination of the taxon inconsistency file it would seem that these two processes are not disjoint in principle, though they currently are recorded as being disjoint in GO. <br />
<br />
* According to current thinking, the cellular process term covers processes occurring at the cellular level in a single organism. <br />
* Multi-organism process covers processes that involve more than one organism. <br />
* These two processes are considered disjoint (mutually exclusive), and so cannot have is_a children in common.<br />
<br />
So the question is, where do we put processes ocurring at the cellular level, and including multiple organisms? Examples are 'receptor mediated endocytosis of virus by host' and 'viral transcription'. The process 'receptor mediated endocytosis of virus by host' clearly happens at the cellular level but requires the participation of viral gene products, and so is a cellular multi-organism process. We cannot currently make the term 'cellular multi-organism process' because it would be an is_a child of both multi-organism process and cellular process. This is not allowed, as the two parent terms are disjoint. <br />
<br />
This stucture is not permitted as the two parent terms are disjoint:<br />
<br />
[i]cellular process<br />
---[i]cellular multi-organism process<br />
[i]multi-organism process<br />
---[i]cellular multi-organism process<br />
<br />
Somehow we have to decide whether to place 'receptor mediated endocytosis of virus by host' under cellular process or multi-organism process, but it doesn't make sense to choose, as it is clearly happening at the cellular level, and involves two organisms. <br />
<br />
Currently we have terms that should be descendents of cellular multi-organism process placed as descendents of cellular process, and they have virus annotations. As we start to make more virus annotations, it is inevitable that there will be more terms like this. Such terms are immediately flagged up if a taxon rule is made as follows:<br />
<br />
[Term]<br />
id: GO:0009987<br />
name: cellular process<br />
relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms<br />
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(Cellular organisms excludes viruses.)<br />
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It would be helpful to resolve this problem at some point, but this can only be done if the multi-organism process and cellular process are no longer stipulated to be disjoint from one another.<br />
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===Proposal 1===<br />
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I would like to propose that the disjoint relationship between cellular process and multi-organism process be removed, and a child term cellular multi-organism process be created. <br />
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==Direct or indirect viral annotations to cellular process should be allowed==<br />
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Following on from the proposal above, if a viral annotation was made to a term such as 'receptor mediated endocytosis of virus by host' and then slimmed up to cellular process, then the annotation would be wrong according to current thinking. (Current GO community understanding is that cellular processes can only be carried out by gene products of cellular organisms, and viruses are not cellular organisms.) <br />
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===Proposal 2===<br />
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I would like to propose that the term cellular process should not be restricted to use only for annotation of gene products of cellular organisms, either in the taxon checking file or in the definition or established understanding of the term. With or without the acceptance of proposal 1, cellular process will still be an ancestor of terms such as 'receptor mediated endocytosis of virus by host' and so it will be as well that annotations should be able to be slimmed up to cellular process without being incorrect.</div>Jdeegan