https://wiki.geneontology.org/index.php?title=Curator_Discussion_Minutes-20080414&feed=atom&action=historyCurator Discussion Minutes-20080414 - Revision history2024-03-28T17:05:42ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Curator_Discussion_Minutes-20080414&diff=50267&oldid=prevGail at 22:29, 22 April 20142014-04-22T22:29:06Z<p></p>
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<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[Category:Meetings]]</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>I wrote these minutes for our MGI Wiki and thought I would share with the rest of you. Feel free to change, elaborate, etc. <br/></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>I wrote these minutes for our MGI Wiki and thought I would share with the rest of you. Feel free to change, elaborate, etc. <br/></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>-Terry Meehan, Alleles & Phenotypes, MGI, Jackson Laboratory</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>-Terry Meehan, Alleles & Phenotypes, MGI, Jackson Laboratory</div></td></tr>
</table>Gailhttps://wiki.geneontology.org/index.php?title=Curator_Discussion_Minutes-20080414&diff=13059&oldid=prevTmeehan at 18:22, 23 April 20082008-04-23T18:22:26Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>I wrote these minutes for our MGI Wiki and thought I would share with the rest of you. Feel free to change, elaborate, etc. <br/></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>I wrote these minutes for our MGI Wiki and thought I would share with the rest of you. Feel free to change, elaborate, etc. <br/></div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The moderator Mike Cherry started the phone call with an informal roll call. Most of the major MOD were represented including MGI, RGD, SGD, Zfin, Wormbase, Candida Genome Database, Uniprot.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The moderator Mike Cherry started the phone call with an informal roll call. Most of the major MOD were represented including MGI, RGD, SGD, Zfin, Wormbase, Candida Genome Database, Uniprot.</div></td></tr>
</table>Tmeehanhttps://wiki.geneontology.org/index.php?title=Curator_Discussion_Minutes-20080414&diff=13057&oldid=prevTmeehan: New page: I wrote these minutes for our MGI Wiki and thought I would share with the rest of you. Feel free to change, elaborate, etc. <br/> Terry Meehan, Alleles & Phenotypes, MGI, Jackson Laborato...2008-04-23T18:18:59Z<p>New page: I wrote these minutes for our MGI Wiki and thought I would share with the rest of you. Feel free to change, elaborate, etc. <br/> Terry Meehan, Alleles & Phenotypes, MGI, Jackson Laborato...</p>
<p><b>New page</b></p><div>I wrote these minutes for our MGI Wiki and thought I would share with the rest of you. Feel free to change, elaborate, etc. <br/><br />
Terry Meehan, Alleles & Phenotypes, MGI, Jackson Laboratory<br />
<br />
The moderator Mike Cherry started the phone call with an informal roll call. Most of the major MOD were represented including MGI, RGD, SGD, Zfin, Wormbase, Candida Genome Database, Uniprot.<br />
<br />
=== Discussion of C. Elegans paper by Andrei Petcherski of Wormbase ===<br />
<br />
''' Brief discussion about wormbase annotation process ''' <br/><br />
1. Use GO terms <br/><br />
2. Look for specific techniques (transgene, RNAi, mutational analysis) <br/><br />
3. Note what figures is relevant for each <br/><br />
''' Interesting figure on break down of database ''' <br/><br />
1. 4,232 papers annotated <br/><br />
2. Largest category is expression data (1219) followed by RNAI (938) <br/><br />
3. Organism Identification<br />
<br/><br />
=== Metadata ===<br />
During discussion of C. elegans paper, Mary of RGD asked if other curators had problems with identification of the species of origin for a given protein or gene used in a paper. This generated a great deal of discussion:<br />
<br />
==== Reasons for absence of information ====<br />
1. RGD finds many researches treat rat and mouse as the same thing <br/><br />
2. Speculation that authors want to blur distinction so their research has more relevance to human disease <br/><br />
3. Others pointed out that many researchers don<nowiki>’</nowiki>t know what the species of origin; they simply have an expression vector in a tube labeled "Beta-Actin" <br/><br />
4. To people in a particular subfield like reviewers, it may be obvious the species of origin <br/><br />
5. Many researchers don<nowiki>’</nowiki>t care <br/><br />
<br />
==== Lack of species origin data creates problems in database ====<br />
1. Time spent by curators on this issues is a waste of resources <br/><br />
* At the protein-protein interaction database, 50% of curators time is spent trying to figure this out <br/><br />
2. good research is left out of databases <br/><br />
==== Metadata to collect ====<br />
1. Authors should include at a minimum identifiers for the protein(s) or gene(s)used<br />
* There was almost universal consensus for this<br />
* TAIR and Plant Physiology collaboration<br />
* PLOS journals are moving towards collecting metadata<br />
2. Other pieces of metadata to include would be strain identification, alleles, and isoforms<br />
* Curators agreed its helpful but if you ask for too much, you<nowiki>’</nowiki>ll get nothing<br />
* Strain data is often misunderstood by researchers<br />
* Metadata collection and enforcement<br />
<br />
==== Debate whether there should be a central database or leave it in charge of individual journals ====<br />
1. Central database would allow for improvements in data collection form without consulting journals<br />
* Specific forms could be tailored to different areas of research<br />
* Changes to forms could be made quickly<br />
* Central gathering site is more stable<br />
2. Journals should collect metadata<br />
* Most journals would not give up control<br />
* Too many forms at a central site would generate confusion<br />
* Journals should instead be convinced to collect metadata as part of their manuscript submission process<br />
* Journals have more enforcement power<br />
* Discussion also included where metadata should be placed: into the methods section, including it in the keywords, having it on the journal website.<br />
==== Convincing Journals to collect metadata ====<br />
1. Curators should present a united front<br />
* Start generating a letter<br />
* Further need for a biocurator society<br />
2. Benefits to journal<br />
* Makes journals more "searchable" by data-mining software<br />
* Curated papers will get more hits<br />
* SGD actually tracks how many people go to pubmed or journal homepages from their website (METRICS)<br />
3. Raising awareness<br />
* Get the scientific community involved<br />
* Protein Structure Database resulted from the community realizing benefits of IDs<br />
* Writing editorials<br />
* Meetings<br />
* Think of further ways could benefit authors</div>Tmeehan