https://wiki.geneontology.org/api.php?action=feedcontributions&user=Simont&feedformat=atomGO Wiki - User contributions [en]2024-03-28T09:22:15ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=RGD_November_2011&diff=23362RGD November 20112009-12-08T19:50:08Z<p>Simont: Created page with '== RGD, The Rat Genome Database, December 2009 == === 1. Staff working on GOC tasks === RGD Admin: Simon Twigger, Mary Shimoyama GO Curators: Stan Laulederkind, Tom Hayman, Ti…'</p>
<hr />
<div>== RGD, The Rat Genome Database, December 2009 ==<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
RGD Admin: Simon Twigger, Mary Shimoyama<br />
<br />
GO Curators: Stan Laulederkind, Tom Hayman, Tim Lowry, Victoria Petri, Shur-Jen Wang<br />
(2.5 fte, 0.8 funded by NHGRI GOC grant)<br />
<br />
IT staff associated with GO related projects such as the development of the online curation tool and of pipelines, the updates/loads of GO ontologies in the database and the generation and submission of RGD Gene Association files: <br />
Jeff DePons<br />
(1 fte, 0 fte funded by NHGRI grant)<br />
<br />
=== 2. Annotation progress ===<br />
<br />
{| border="1" cellspacing="0" cellpadding="5" align="center"<br />
! Gene Products<br />
! Annotations 2008<br />
! Annotations 2009<br />
! % Change<br />
|- <br />
| 20466<br />
| 169,127<br />
| 191,323 (109127 non-IEA)<br />
| +13%<br />
|-<br />
|}<br />
<br />
<br />
Based on a review of the GOC gene_association.rgd files from November 2008 and December 2009, the total number of annotations from RGD has increased from 81980 to 102,728, an increase of 20,748 (25%), with annotations for 11,652 gene products (+843, 8% from 2008). The number of manual annotations from RGD has increased from 23,555 to 30,418 (+6,863 annotations, 29%) and the number of genes with manual annotations has increased from 4,785 to 5,362 (+577, 12%). Significant changes this year include the change in evidence code for our automated ortholog pipelines that map GO annotations from mouse orthologs. These were previously listed as ISS but this was changed to ISO following the evidence code guidelines.<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
Because the pipelines for GO annotations are automated and updated weekly, all of the curators’ efforts are involved in manual annotation. Although RGD curators also annotate to other ontologies, approximately 75% of their curation efforts are related to GO annotations<br />
<br />
a. Literature curation: RGD targets gene sets for manual curation and all rat papers published about those genes are curated. In 2009, there have been 3 major types of gene datasets curated:<br />
<br />
# disease related: diabetes genes <br />
# genes which are part of the Reference Genome Annotation Project<br />
# genes involved in targeted metabolic, signaling, regulatory, and disease pathways.<br />
<br />
b. Computational annotation strategies:<br />
<br />
# Rat genes manually curated by other groups are brought in electronically from GOA with their associated evidence codes and the originating group acknowledged in the source.<br />
# ISO - RGD is not currently doing manual annotation with ISO. ISO annotations are created through our automated pipelines that map GO annotations from mouse genes over to their Rat orthologs. For each mouse gene that has a confirmed rat ortholog, if the GO annotation to the Mouse gene is of evidence type IDA, IMP, IPI, IGI or IEP then the annotation is loaded onto the rat ortholog as an ISO annotation.<br />
# IEA - rat annotations based on GO mapping to InterPro, Enzyme Commission and Swiss-Prot keywords, are brought in electronically with IEA evidence code from GOA. Annotations from GOA for all categories are updated weekly.<br />
<br />
c. Priorities for annotation: There are several ways in which RGD assigns priorities for the annotation of genes to GO ontology terms. These include: the genes in the monthly list for the Reference Genome Annotation Project, genes associated with targeted disease, and genes involved in particular pathways.<br />
<br />
=== 4. Presentations and publications ===<br />
<br />
<br />
a. Papers with substantial GO content<br />
<br />
# Reference Genome Group of the Gene Ontology Consortium. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species, PLoS Comput Biol. 2009 Jul;5(7):e1000431. (PMCID: PMC2699109)<br />
# The Rat Genome Database 2009: variation, ontologies and pathways. Nucleic Acids Res. 2009 Jan;37(Database issue):D744-9 (PMCID: PMC2686558)<br />
<br />
<br />
b. Presentations including Talks and Tutorials and Teaching <br />
<br />
# Simon Twigger and Jennifer Smith taught lectures on Ontologies and the Gene Ontology as part of the Bioinformatics: Tools and Tactics course, a component of the Physiology Ph.D. program at the Medical College of Wisconsin.<br />
# Rat Genomics & Models, December 2 - 5, 2009, Cold Spring Harbor, NY, Workshop: "Rat Genome Database" - Presentations featuring use of gene ontology on the RGD website.<br />
# Rat Genomics & Models, December 2 - 5, 2009, Cold Spring Harbor, NY, Presentation: "The Rat Genome Database Genome Viewer" - Presentation featuring gene ontology information accessed through the RGD genome viewer.<br />
<br />
<br />
c. Poster presentations<br />
<br />
# MCW Research Day, September 16, 2009, Milwaukee, WI - poster presenting information about RGD gene report pages prominantly featuring gene ontology annotations.<br />
# Rat Genomics & Models, December 2 - 5, 2009, Cold Spring Harbor, NY Poster: "Multiple ontologies for prioritizing and standardizing biological information at the Rat Genome Database"<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. GO terms contributed by RGD'''<br />
<br />
RGD has contributed 23 new terms to GO this year.<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
<br />
'''C. Other highlights'''<br />
<br />
Ontology Education Video tutorials, available on Scivee.tv, YouTube and Vimeo.com developed in conjunction with the NCBO<br />
<br />
* [http://www.scivee.tv/node/11759 Introduction to Biomedical Ontologies #1] - What is an Ontology (Viewed 2501 times to date across all three video sites)<br />
* [http://www.scivee.tv/node/12395 Introduction to Biomedical Ontologies #2] - Anatomy of an Ontology Annotation (Viewed 807 times to date across all three video sites)<br />
* [http://www.scivee.tv/node/14306 Introduction to Biomedical Ontologies #3] - Anatomy of an Ontology Annotation, Part 2 (Viewed 198 times to date across all three video sites)</div>Simonthttps://wiki.geneontology.org/index.php?title=Grant_Progress_Reports_December_2009&diff=23361Grant Progress Reports December 20092009-12-08T19:50:02Z<p>Simont: </p>
<hr />
<div>=== Working Groups ===<br />
<br />
[[Ontology Development Progress Report December 2009]]<br />
<br />
[[Outreach and Advocacy Progress Report December 2009]]<br />
<br />
=== MODs and Annotation Projects ===<br />
<br />
[[MGI]]<br />
<br />
[[WormBase]]<br />
<br />
[[EcoliWiki]]<br />
<br />
[[RGD]]<br />
<br />
=== Supplements ===<br />
<br />
[[Princeton Progress Report December 2009]]<br />
<br />
[[Sequence Ontology Progress Report December 2009]]</div>Simonthttps://wiki.geneontology.org/index.php?title=2009_Cambridge_Meeting_Logistics&diff=219992009 Cambridge Meeting Logistics2009-09-16T14:06:20Z<p>Simont: </p>
<hr />
<div>=Latest updates=<br />
*[http://maps.google.com/maps/ms?ie=UTF&msa=0&msid=115043168235550753357.000473b124c276830ad23 New map available], with Jesus College and the two restaurants in town highlighted<br />
*The arrival dinner on Tuesday, Sept. 24th, will start at 7:30 PM.<br />
=Dates=<br />
GO consortium & SAB meetings September 23-25, 2009<br />
<br />
=Venue=<br />
Meetings, lodging and some meals will be in [http://conference.jesus.cam.ac.uk Jesus College], Cambridge, UK.<br />
<br />
Meetings will be held in the Upper Hall room, and meals will be served in the the Prioress's Room.<br />
<br />
==Maps==<br />
[http://www.cam.ac.uk/map/ Official Cambridge University map]<br />
<br />
Portion of Cambridge University map showing Jesus College [http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=main;xx=1900;yy=560;gf=png view 1] [http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=main;xx=2017;yy=535;mt=c;ms=150;tl=Jesus%20College view 2]<br />
<br />
Other selections from the Cambridge University map:<br />
*[http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=main;xx=1900;yy=1040 central Cambridge]<br />
*[http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=region Cambridge and surrounding region]<br />
<br />
Google Maps:<br />
*[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=jesus+college,+cambridge+cb5+8bl,+uk&sll=52.208198,0.123575&sspn=0.009296,0.012617&ie=UTF8&ll=52.208751,0.122824&spn=0.009296,0.012617&z=16 Jesus College]<br />
*[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=183+east+road,+cambridge+cb1+1bg,+uk&sll=52.204522,0.133312&sspn=0.009297,0.012617&ie=UTF8&ll=52.204609,0.133209&spn=0.009297,0.012617&z=16&iwloc=A Cotto], 183 East Road (Tuesday dinner venue)<br />
*[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=quayside,+cambridge,+uk&sll=52.261854,0.083771&sspn=0.297125,0.403748&ie=UTF8&ll=52.209803,0.117202&spn=0.009296,0.012617&z=16 Cambridge Quayside] (location of River Bar & Kitchen, Thursday dinner venue)<br />
<br />
=Registration=<br />
Registration is now open, via [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 web form].<br />
<br />
'''Deadline:''' Please register by '''September 4''' if you want to stay at Jesus College (more info below), or by '''September 14''' if you don't need accommodation. If you miss the deadline, we can try to squeeze you into the meeting room, but you'll be on your own not only for lodging, but also for all meals, including lunch.<br />
<br />
Note that there is a table of attendees below, but this time we are using it only to gather arrival and departure information for airport ride shares. '''You must register using the online form.'''<br />
<br />
Additional note about the registration form: there is a page that asks about pick-up and drop-off, but it's only there because we're using a standardized EMBL web form. For these meetings, please just skip that page (it has a "Skip" button).<br />
<br />
==Registration Fee==<br />
Fees and payment methods are noted on the [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 registration form]. Quick summary:<br />
<br />
*GBP 109.20 (about $177 as of July 10) for both meetings Sept. 23-25<br />
*GBP 72.80 for only the GO Consortium meeting Sept. 23-24<br />
*GBP 36.40 for only the SAB meeting Sept. 25<br />
<br />
Payable by credit card or bank transfer (note to US participants: if you're considering paying by bank transfer, check with your bank first to find out how much they charge for an international transfer, as some charge quite a bit); [[#Contact|contact]] us if you have problems or questions about paying.<br />
<br />
A receipt will be provided.<br />
<br />
=Lodging Information (deadline Sept. 4)=<br />
'''Please note that the deadline to reserve accommodation at Jesus College has passed. If you have not already booked a college room, you will have to arrange your own accommodation elsewhere in Cambridge.'''<br />
<br />
We have reserved 40 single ensuite bedrooms in Jesus College from September 22 (check-in) to 26 (check-out), 2009. Room booking is part of the [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 registration form]; all you have to do is check the boxes for the dates you'll need a room.<br />
<br />
Rate: GBP 59.50 per night (about $97 as of July 10)<br><br />
This includes breakfast and wireless network, and is payable with your meeting registration fee.<br />
<br />
Deadline: '''September 4, 2009'''<br><br />
After Sept. 4, you will still be able to register for the meeting, but you will have to arrange your own lodging. If you need suggestions, please get in touch with Holly or Midori ([[#Contact|see below]]).<br />
<br />
=Food=<br />
You can indicate dietary restrictions on the [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 registration form].<br />
<br />
Lunch will be provided by Jesus College on all three days.<br />
<br />
Dinners are noted on the registration form. Quick summary:<br />
*Tuesday, Sept. 22: Arrival dinner at [http://www.cottocambridge.co.uk/ Cotto], Cambridge<br />
**Time: 7:30 PM<br />
**Menu: Choose from the small selection on the evening.<br />
*Wednesday, Sept. 23: Dinner at Jesus College<br />
*Thursday, Sept. 24: Dinner at [http://www.riverbarkitchen.com River Bar & Kitchen], Cambridge<br />
**Time: 7:30 PM<br />
**Menu: Pre-order by '''September 22''' (Tuesday) from the [http://www.riverbarkitchen.com/menuParty.asp?pre-order=1 set menu for parties]. Note: don't fill out the restaurant web form; we'll collect your selections by email after you've registered.<br />
*Friday, Sept. 25: Dinner at Jesus College<br />
<br />
When you [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 register], please sign up for all dinners that you plan to attend. For the two restaurant dinners, the cost of the food is payable with your registration fee and will appear on your registration receipt. Drinks are not included, and must be paid separately on the night (we'll collect as we've done at a few recent GO dinners).<br />
<br />
=Managing Remote Participation=<br />
We plan to offer remote access along roughly the same lines as at the last GOC meeting in Oregon: We'll use a combination of the GO Ready Conference and Stanford's WebEx to allow remote attendees to participate. The meeting room will be equipped with a single conference phone, plus the usual projector and screen. Remote attendees will be asked to mute their lines unless they would like to speak. Someone will be monitoring remote attendees either on the WebEx 'raise your hand' feature or on a skype chat to ensure that remote attendees get an opportunity to be heard. All presenters are asked to use their mouse to interact with their slides so the WebEx participants can see what you are pointing to. Where possible we encourage remote participants to share a single connection to the teleconference as this will reduce the number of connections and likely increase the sound quality for everyone.<br />
<br />
=Transportation=<br />
Cambridge University [http://www.cam.ac.uk/visitors/gettingto.html "Getting to Cambridge" page]<br />
<br />
Train and bus transport is available from the major London airports. Or, if there are three or more people arriving or departing together, it can be time- and cost-effective to share a pre-booked taxi. Contact us if you would like a quote or for us to book a taxi. Note: '''do not''' take a taxi from Heathrow or Gatwick without booking in advance -- it's staggeringly expensive.<br />
<br />
Also note the registration form there is a page that asks about pick-up and drop-off, but it's only there because we're using a standardized EMBL web form. For these meetings, you can skip that page (it has a "Skip" button).<br />
<br />
=Things To Do=<br />
[http://www.visitcambridge.org/ Official Cambridge tourism site]<br />
<br />
[http://www.cam.ac.uk/visitors/ Cambridge University Visitors page]<br />
<br />
[http://www.cam.ac.uk/visitors/places.html Cambridge University "places and events to visit" page]<br />
<br />
=Attendees=<br />
Please [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 register online].<br />
<br />
Please fill in the Arrival and Departure table below if you would like to try a carpool to/from the airport.<br />
<br />
Airport codes: LHR = Heathrow; LGW = Gatwick; STN = Stansted; LTN = Luton; LCY = London City<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time to Airport (see codes above)<br />
! Departure Date/Time from Airport<br />
|-<br />
| Judy Blake<br />
| GO / MGI<br />
|Sept 22 / AA 108 arr 6:50 am to LHR<br />
|Sept 27 / AA 109 dep 10:55 am from LHR<br />
|-<br />
| Brenley McIntosh<br />
| EcoliWiki<br />
| Sept 18 arr 9:35am to LHR<br />
| Sept 28 dep 8:40am from LHR<br />
|-<br />
| Pascale Gaudet<br />
| dictybase<br />
| Sep 22 06:20 UA 958 LHR<br />
| Sep 26 12:20 from LHR<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Sep 22 arr 06:50 AA 86 LHR<br />
| Sep 25 dep 12:50 AA 47 LHR<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Sept 22 arr 10:15AM CO 110 LHR<br />
| Sept 27 dep 10:25AM CO 29 LHR<br />
|-<br />
|}<br />
<br />
=Remote Attendees=<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! email (needed to set up your remote access)<br />
! Attending GOC (Sept. 23-24)<br />
! Attending SAB (Sept. 25)<br />
! Calling in alone or in a group (with whom and from where, if known)<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Peter.D'Eustachio@nyumc.org<br />
| yes<br />
| ?<br />
| alone<br />
|-<br />
| Marcus Chibucos<br />
| Institute for Genome Sciences<br />
| mchibucos at som dot umaryland dot edu<br />
| yes<br />
| not sure<br />
| Michelle Gwinn-Giglio from IGS (Baltimore, MD, USA)<br />
|-<br />
|Harold Drabkin<br />
|MGI<br />
|hjd@informatics.jax.org<br />
|yes<br />
|yes<br />
|unsure<br />
|-<br />
|Michelle Giglio<br />
|Institute for Genome Sciences<br />
|mgiglio at som dot umaryland dot edu<br />
|yes<br />
|only for PM GO clinic<br />
|depending on how the times work out - may be along with Marcus at IGS (Baltimore) or alone at home<br />
|-<br />
|Alexander Diehl<br />
|MGI<br />
|adiehl@informatics.jax.org<br />
|yes<br />
|yes<br />
|unsure<br />
|-<br />
|Amina Abdulla<br />
|LBL BerkeleyBOP<br />
|aabdulla [at] berkeleybop [dot] org<br />
|yes<br />
|yes<br />
|Alone - work and home<br />
|-<br />
|Mary Dolan<br />
|MGI<br />
|mdolan@informatics.jax.org<br />
|yes<br />
|yes<br />
|unsure<br />
|-<br />
-<br />
|Kara Dolinski<br />
|Princeton<br />
|kara@genomics.princeton.edu<br />
|yes<br />
|unsure<br />
|unsure<br />
|-<br />
|Li Ni<br />
|MGI<br />
|adiehl@informatics.jax.org<br />
|yes<br />
|yes<br />
|alone - home<br />
|-<br />
|Lakshmi Pillai<br />
|AgBase<br />
|pillai@cvm.msstate.edu<br />
|yes<br />
|no<br />
|unsure<br />
|-<br />
|Ranjana Kishore<br />
|WormBase<br />
|ranjana@caltech.edu<br />
|yes<br />
|maybe<br />
|alone - home or work<br />
|-<br />
|Simon Twigger<br />
|RGD<br />
|simont@mcw.edu<br />
|hopefully<br />
|yes<br />
|alone - home or work<br />
|-<br />
<br />
<br />
=Contact=<br />
'''Please contact Midori Harris (midori at ebi dot ac dot uk) or Holly Foster (nee Edwards) (holly dot edwards at ebi dot ac dot uk) if you have any questions.'''<br />
<br />
[[Category:Meetings]]</div>Simonthttps://wiki.geneontology.org/index.php?title=Register&diff=12025Register2008-03-20T17:04:45Z<p>Simont: /* Registration for April 2008 GO Meetings at University of Utah, SLC */</p>
<hr />
<div>===Registration for April 2008 GO Meetings at University of Utah, SLC===<br />
<br />
Please register here giving information about which meetings you will be attending. <br />
We are asking for 'years on the project' because this is the 10th year of the GOC and we want to celebrate.<br />
<br />
{|border="1" cell spacing="0" cellpadding="5" align="left"<br />
!Name <br />
!Institution <br />
!Model Organism(s) and/or Speciality <br />
!Years on GOC project <br />
!Role on GOC project <br />
!Coming to Ref Genome? <br />
!Coming to GOC? <br />
!Where are you staying? <br />
!food requirement<br />
|-<br />
|Sue Rhee<br />
|The Arabidopsis Information Resource (TAIR)<br />
|Arabidopsis<br />
|8 years<br />
|Co-PI<br />
|No<br />
|Yes<br />
|not arranged yet<br />
|<br />
|-<br />
|Karen Eilbeck<br />
|University of Utah<br />
|Sequences<br />
|5 years<br />
|SO manager<br />
|yes<br />
|yes<br />
|Home<br />
|veggie<br />
|-<br />
|Judy Blake<br />
|The Jackson Laboratory<br />
|mouse /genomics<br />
|10 years<br />
|PI <br />
|yes<br />
|yes<br />
|University GuestHouse<br />
|<br />
|-<br />
|Suzanna Lewis<br />
|Lawrence Berkeley National Laboratory<br />
|Bioinformatics / fly<br />
|10 years<br />
|PI<br />
|yes<br />
|yes<br />
|?<br />
|<br />
|-<br />
|Harold Drabkin<br />
|The Jackson Laboratory<br />
|mouse / biochemistry<br />
|7 years<br />
|BioCurator<br />
|yes<br />
|yes<br />
|not arranged yet<br />
|<br />
|-<br />
|Amelia Ireland<br />
|GO Editorial Office, EBI<br />
|Jack of all trades<br />
|6<br />
|Senior GO Curator<br />
|yes<br />
|yes<br />
|hopefully not on the streets<br />
|<br />
|-<br />
|Jennifer Deegan<br />
|GO Editorial Office, EBI<br />
|Large scale content efforts. <br />
|5 years<br />
|Ontology Editor, Outreach/Advocacy Manager<br />
|No<br />
|Yes<br />
|Little America<br />
|No restrictions<br />
|-<br />
|Daniel Barrell<br />
|EMBL - The EBI<br />
|UniProt/Human/Chicken/Cow<br />
|7 years<br />
|GOA database programmer<br />
|No<br />
|Yes<br />
|Little America<br />
|none<br />
|-|<br />
|David Hill<br />
|The Jackson Laboratory<br />
|mouse/developmental biology/ontology content<br />
|9 years<br />
|MGI curator/ Ontology Development Co-manager<br />
|yes<br />
|yes<br />
|Not arranged yet<br />
|<br />
|-<br />
|Midori Harris<br />
|GO Editorial Office, EBI<br />
|GO content, especially trying to keep up with ordinary SourceForge submissions<br />
|9.5 years<br />
|GO Editor; ontology development co-manager<br />
|yes<br />
|yes<br />
|University Guest House<br />
|no restrictions<br />
|-<br />
|Pascale Gaudet<br />
|Northwestern University<br />
|dictyBase curator<br />
|5 years<br />
|annotation/reference genomes/ontology content/AmiGO-WPWG<br />
|yes<br />
|yes<br />
|Not arranged yet<br />
|<br />
|-<br />
|Tanya Berardini<br />
|The Arabidopsis Information Resource<br />
|Arabidopsis/developmental biology/ontology content<br />
|6 years<br />
|annotation/reference genomes/ontology development/OBO-Edit working group/annotation outreach<br />
|yes<br />
|yes<br />
|Not arranged yet<br />
|<br />
|-<br />
|Mary Dolan<br />
|MGI, The Jackson Laboratory<br />
|Mouse<br />
|5 years<br />
|computational methods/tool development/software<br />
|yes<br />
|yes<br />
|University GuestHouse<br />
|none<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase, Caltech<br />
|C. elegans<br />
|5 years<br />
|curator/user advocacy (gohelp)/software development for semi-automated curation<br />
|yes<br />
|yes<br />
|University Guest House<br />
|none<br />
|-<br />
|Mike Cherry<br />
|SGD, Stanford<br />
|S. cerevisiae<br />
|10 years<br />
|PI<br />
|yes<br />
|yes<br />
|University Guesthouse (to be arranged)<br />
|none<br />
|-<br />
|Doug Howe<br />
|ZFIN, U. Oregon<br />
|D. rerio<br />
|4.5 years<br />
|Ontology development/Ref. Genome/GO annotation<br />
|Yes<br />
|Yes<br />
|University GuestHouse<br />
|<br />
|-<br />
|Stacia Engel<br />
|SGD, Stanford<br />
|S. cerevisiae<br />
|6 years<br />
|Curator/refGenome<br />
|yes<br />
|yes<br />
|University Guesthouse (to be arranged)<br />
|<br />
|-<br />
|Susan Tweedie<br />
|FlyBase, University of Cambridge<br />
|Drosophila<br />
|2 years<br />
|GO annotation/ref. genome/newsletter team<br />
|yes<br />
|yes<br />
|University Guesthouse<br />
|veggie<br />
|-<br />
|Seth Carbon<br />
|Berkeley BOP<br />
|AmiGO/Software<br />
|~1 1/2<br />
|AmiGO/Software and related WGs<br />
|yes<br />
|yes<br />
|TBD<br />
|none<br />
|-<br />
| Valerie Wood<br />
| WT Sanger Institute<br />
| S. pombe MOD DB project manager<br />
| 8<br />
| S. pombe / GO curator/ ref genomes group/ AWG (retired!)<br />
| yes<br />
| yes<br />
| TBD <br />
| none<br />
|-<br />
|Fiona McCarthy <br />
|Mississipi State University (AgBase)<br />
|chicken & cow <br />
|3 sort of<br />
|associate GOC member, chick Ref genome, Outreach<br />
|yes <br />
|yes<br />
|TBD<br />
|<br />
|-<br />
|Ranjana Kishore<br />
|WormBase, Caltech<br />
|C. elegans<br />
|5<br />
|Curator/Annotation, Ref genomes, Outreach<br />
|yes<br />
|yes<br />
|University Guesthouse<br />
|veggie<br />
<br />
|-<br />
|Chris Mungall<br />
|LBNL<br />
|<br />
|8<br />
|Software Manager<br />
|yes<br />
|yes<br />
|?<br />
|veggie<br />
|-<br />
|Donghui Li<br />
|TAIR<br />
|Arabidopsis/ontology content<br />
|2 years<br />
|annotation/reference genomes/ontology development<br />
|yes<br />
|yes<br />
|not arranged yet<br />
|veggie<br />
|-<br />
|Emily Dimmer<br />
|GOA<br />
|Human<br />
|4.5 years<br />
|curator/GOA co-ordinator<br />
|yes<br />
|yes<br />
|University GuestHouse<br />
|<br />
|-<br />
|Jim Hu<br />
|EcoliWiki/EcoliHub and GONUTS<br />
|''E. coli''<br />
|1.5 years<br />
|E. coli for RefGenome<br />
|yes<br />
|no (have to teach)<br />
| University Guesthouse<br />
|Lac<sup>-</sup><br />
|-<br />
|Debby Siegele<br />
|EcoliWiki/EcoliHub<br />
|''E. coli''<br />
|1 year<br />
|E. coli for RefGenome<br />
|yes<br />
|no<br />
| University Guesthouse<br />
|<br />
|-<br />
|Rex Chisholm<br />
|dictyBase<br />
|D. discoideum<br />
|9 years<br />
|co-PI/reference genomes<br />
|yes<br />
|yes<br />
|University Guesthouse<br />
|<br />
|-<br />
|Michelle Gwinn Giglio<br />
|Institute for Genome Sciences<br />
|prokaryotes<br />
|7 years<br />
|annotator/term developer/PAMGO/outreach group/evidence group<br />
|no<br />
|yes<br />
|University Guest House<br />
|<br />
|-<br />
|Victoria Petri<br />
|Rat Genome Database<br />
|rat / biochemistry<br />
|4.5 years<br />
|GO annotations/Ref. Genomes/Newsletter team/Term contributions<br />
|yes<br />
|yes<br />
|University Guest House<br />
|none<br />
|-<br />
|Alex Stoddard<br />
|Rat Genome Database<br />
|rat / bioinformatics<br />
|0.5 years<br />
|RGD software development<br />
|yes<br />
|yes<br />
|University Guest House<br />
|<br />
|-<br />
|Siddhartha Basu<br />
|dictyBase<br />
|dictyBase software developer<br />
| 3 months<br />
| Reference Genomes<br />
| yes<br />
| yes<br />
| Not yet<br />
| None<br />
|-<br />
<br />
|Ramana Madupu<br />
|J Craig Venter Institute<br />
|prokaryotes<br />
| 3 months<br />
| annotator/JCVI representative<br />
| no<br />
| yes<br />
| Not yet<br />
| vegetarian<br />
|-<br />
|Jane Lomax<br />
|GO Editorial Office, EBI<br />
|Content, mappings<br />
|6 years<br />
|Ontology Editor, Outreach/Advocacy Manager<br />
|No<br />
|Yes<br />
|?<br />
|<br />
|-<br />
|Scott Durkin<br />
|J Craig Venter Institute<br />
|Prokaryotes<br />
|3 months<br />
|Annotator/JCVI representative<br />
|No<br />
|Yes<br />
|Not yet<br />
|None<br />
|-<br />
|Peter D'Eustachio<br />
|Reactome / New York University<br />
|human<br />
|about 3<br />
|content editor<br />
|no<br />
|yes<br />
|University guesthouse<br />
|none<br />
|-<br />
|Simon Twigger<br />
|Rat Genome Database (RGD)<br />
|Rat<br />
|6 years<br />
|Co-PI<br />
|No<br />
|Yes<br />
|University Guest House<br />
|no restrictions<br />
|<br />
|}<br />
<br />
<br />
[[SLC_GO_Consortium_Meeting|SLC Consortium meeting]] |<br />
[[SLC_GO_Reference_Genome_Project_Meeting|SLC Ref Genomes meeting]] | [[GO_Field_Trip|SLC field trip]] |<br />
[[Consortium_Meetings|Consortium meetings main page]]</div>Simonthttps://wiki.geneontology.org/index.php?title=External_Database_Contact_Info_(Archived)&diff=11564External Database Contact Info (Archived)2008-02-18T19:04:22Z<p>Simont: /* RGD */</p>
<hr />
<div>Many groups associated with and outside the GOC consume the resources produced by GO, such as the gene_ontology_edit.obo file and the association files. Any major changes to these files are signaled in advanced on the gofriends list. We also would like to track the persons in charge of the technical aspects of the various different MOD databases in order to make sure they are prepared for forthcoming changes.<br />
<br />
== dictyBase ==<br />
<br />
* siddhartha-basu AT northwestern DOT edu<br />
* pgaudet AT northwestern DOT edu<br />
<br />
Schema: Chado<br />
<br />
== SGD ==<br />
<br />
* Ben Hitz ( hitz AT genome DOT stanford AT edu)<br />
* Mike Cherry (cherry AT stanford DOT edu)<br />
<br />
== RGD ==<br />
<br />
Curation<br />
* Victoria Petri vpetri at mcw dot edu<br />
* Mary Shimoyama shimoyama at mcw dot edu<br />
<br />
Technical<br />
* Alex Stoddard (astoddard at mcw dot edu)<br />
<br />
Admin<br />
* Simon Twigger simont at mcw dot edu<br />
<br />
== MGI ==<br />
<br />
* David Miers <dbm AT informatics DOT jax DOT org><br />
* Jim Kadin <jak AT informatics DOT jax DOT org><br />
<br />
==UniProtKB ==<br />
<br />
* Dan Barrel<br />
* David Binns?<br />
<br />
== WormBase ==<br />
<br />
== FlyBase ==<br />
<br />
* Paul?<br />
* Susan?<br />
<br />
Schema: Chado<br />
<br />
== GR (Gramene) ==<br />
<br />
* <br />
* Pankaj?<br />
<br />
== SPombe/GeneDB_* ==<br />
<br />
* Val?<br />
<br />
== NCBI ==<br />
<br />
* ?<br />
<br />
== E Coli ==<br />
<br />
* Jim Hu?<br />
<br />
== ZFIN ==<br />
<br />
* Sierra Moxon?<br />
* Doug?<br />
<br />
== TAIR ==<br />
<br />
== ==</div>Simonthttps://wiki.geneontology.org/index.php?title=External_Database_Contact_Info_(Archived)&diff=11563External Database Contact Info (Archived)2008-02-18T19:02:01Z<p>Simont: /* RGD */</p>
<hr />
<div>Many groups associated with and outside the GOC consume the resources produced by GO, such as the gene_ontology_edit.obo file and the association files. Any major changes to these files are signaled in advanced on the gofriends list. We also would like to track the persons in charge of the technical aspects of the various different MOD databases in order to make sure they are prepared for forthcoming changes.<br />
<br />
== dictyBase ==<br />
<br />
* siddhartha-basu AT northwestern DOT edu<br />
* pgaudet AT northwestern DOT edu<br />
<br />
Schema: Chado<br />
<br />
== SGD ==<br />
<br />
* Ben Hitz ( hitz AT genome DOT stanford AT edu)<br />
* Mike Cherry (cherry AT stanford DOT edu)<br />
<br />
== RGD ==<br />
<br />
* Victoria Petri vpetri at mcw.edu<br />
* Mary Shimoyama shimoyama at mcw.edu<br />
* Simon Twigger simont at mcw.edu<br />
<br />
== MGI ==<br />
<br />
* David Miers <dbm AT informatics DOT jax DOT org><br />
* Jim Kadin <jak AT informatics DOT jax DOT org><br />
<br />
==UniProtKB ==<br />
<br />
* Dan Barrel<br />
* David Binns?<br />
<br />
== WormBase ==<br />
<br />
== FlyBase ==<br />
<br />
* Paul?<br />
* Susan?<br />
<br />
Schema: Chado<br />
<br />
== GR (Gramene) ==<br />
<br />
* <br />
* Pankaj?<br />
<br />
== SPombe/GeneDB_* ==<br />
<br />
* Val?<br />
<br />
== NCBI ==<br />
<br />
* ?<br />
<br />
== E Coli ==<br />
<br />
* Jim Hu?<br />
<br />
== ZFIN ==<br />
<br />
* Sierra Moxon?<br />
* Doug?<br />
<br />
== TAIR ==<br />
<br />
== ==</div>Simonthttps://wiki.geneontology.org/index.php?title=Cardiovascular_Gene_Page_(Archived)&diff=4097Cardiovascular Gene Page (Archived)2007-09-13T19:53:33Z<p>Simont: /* Useful links */</p>
<hr />
<div>== Useful links ==<br />
<br />
[[Cardiovascular|Return to Cardiovascular Main Page]]<br />
<br />
[[Priority Cardiovascular genes|Priority Cardiovascular Genes Page]] <br />
<br />
[http://www.ucl.ac.uk/medicine/cardiovascular-genetics/geneontology.html UCL cardiovascular page]<br />
<br />
[http://rgd.mcw.edu/dportal/cardiovascular/ Rat Genome Database Cardiovascular Portal for Rat, Human and Mouse genes]<br />
<br />
== The first 50 cardiovascular-associated genes to be annotated as a priority ==<br />
<br />
{|<br />
|width="100" align="center"|'''[[ACHE]]'''||width="100" align="center"|'''[[BAX]]'''||width="100" align="center"|'''[[CTNNB1]]'''||width="100" align="center"|'''[[ELA2]]'''||width="100" align="center"|'''[[HSP90AB1]]'''||width="100" align="center"|'''[[MET]]'''||width="100" align="center"|'''[[PRNP]]'''||width="100" align="center"|'''[[TGFB1]]'''<br />
|-<br />
|align="center"|'''[[ACTG1]]'''||align="center"|'''[[BCL2]]'''||align="center"|'''[[CYCS]]'''||align="center"|'''[[FN1]]'''||align="center"|'''[[HSPA1A]]'''||align="center"|'''[[ORM1]]'''||align="center"|'''[[RAF1]]'''||align="center"|'''[[TNF]]'''<br />
|-<br />
|align="center"|'''[[ADIPOQ]]'''||align="center"|'''[[BRCA1]]'''||align="center"|'''[[DMD]]'''||align="center"|'''[[GCK]]'''||align="center"|'''[[HSPD1]]'''||align="center"|'''[[PAH]]'''||align="center"|'''[[RB1]]'''||align="center"|'''[[TP53]]'''<br />
|-<br />
|align="center"|'''[[ADRB2]]'''||align="center"|'''[[C3]]'''||align="center"|'''[[DUT]]'''||align="center"|'''[[GSK3B]]'''||align="center"|'''[[IGF1]]'''||align="center"|'''[[PKM2]]'''||align="center"|'''[[RPS27A]]'''||align="center"|'''[[TPI1]]'''<br />
|-<br />
|align="center"|'''[[AKT1]]'''||align="center"|'''[[CCR5]]'''||align="center"|'''[[EGF]]'''||align="center"|'''[[HK1]]'''||align="center"|'''[[LEP]]'''||align="center"|'''[[PLG]]'''||align="center"|'''[[SNCA]]'''||align="center"|'''[[TTN]]'''<br />
|-<br />
|align="center"|'''[[ALDOA]]'''||align="center"|'''[[CKB]]'''||align="center"|'''[[EGFR]]'''||align="center"|'''[[HSD3B1]]'''||align="center"|'''[[MAPK14]]'''||align="center"|'''[[PPARG]]'''||align="center"|'''[[SOD1]]'''||align="center"|'''[[YWHAZ]]'''<br />
|-<br />
|align="center"|'''[[APP]]'''||align="center"|'''[[COL1A1]]'''||align="center"|''' '''||align="center"|''' '''||align="center"|''' '''||align="center"|''' '''||align="center"|''' '''||align="center"|''' '''<br />
|}<br />
<br />
== 2538 genes identified as associated with the cardiovascular system ==<br />
<br />
<br />
The gene symbols in red do not have wiki pages created yet.<br />
<br />
[[A4GALT]], [[AACS]], [[AADAT]], [[AARS]], [[AARSD1]], [[AARSL]], [[AASS]], [[ABAT]], [[ABCA1]], [[ABCA2]], [[ABCA4]], [[ABCA8]], [[ABCB10]], [[ABCB4]], [[ABCB6]], [[ABCB7]], [[ABCB8]], [[ABCD2]], [[ABCD3]], [[ABCE1]], [[ABCF1]], [[ABCF2]], [[ABCG1]], [[ABHD10]], [[ABHD4]], [[ACAA1]], [[ACAA2]], [[ACACA]], [[ACACB]], [[ACAD11]], [[ACAD8]], [[ACAD9]], [[ACADL]], [[ACADM]], [[ACADS]], [[ACADSB]], [[ACADVL]], [[ACAT1]], [[ACAT2]], [[ACBD3]], [[ACCN3]], [[ACHE]], [[ACLY]], [[ACN9]], [[ACO2]], [[ACOT1]], [[ACOT11]], [[ACOT12]], [[ACOT2]], [[ACOT4]], [[ACOT7]], [[ACOT8]], [[ACOT9]], [[ACOX1]], [[ACOX2]], [[ACOX3]], [[ACOXL]], [[ACP6]], [[ACSBG1]], [[ACSL1]], [[ACSL3]], [[ACSL4]], [[ACSL5]], [[ACSL6]], [[ACSM1]], [[ACSS1]], [[ACSS2]], [[ACTA1]], [[ACTG1]], [[ACTN2]], [[ACTN3]], [[ACVR1]], [[ACY1]], [[ADAM12]], [[ADAMTS1]], [[ADAMTS10]], [[ADAMTS12]], [[ADAMTS14]], [[ADAMTS15]], [[ADAMTS16]], [[ADAMTS17]], [[ADAMTS18]], [[ADAMTS19]], [[ADAMTS2]], [[ADAMTS20]], [[ADAMTS3]], [[ADAMTS4]], [[ADAMTS5]], [[ADAMTS6]], [[ADAMTS9]], [[ADAMTSL1]], [[ADAMTSL3]], [[ADFP]], [[ADH5]], [[ADI1]], [[ADIPOQ]], [[ADIPOR1]], [[ADIPOR2]], [[ADORA1]], [[ADRA1A]], [[ADRA1B]], [[ADRB2]], [[AEBP1]], [[AES]], [[AFG3L1]], [[AFG3L2]], [[AFMID]], [[AFP]], [[AGC1]], [[AGER]], [[AGMAT]], [[AGPAT1]], [[AGPAT2]], [[AGPAT3]], [[AGPAT4]], [[AGPAT5]], [[AGPAT6]], [[AGPAT7]], [[AGPS]], [[AGRIN]], [[AGT]], [[AGXT]], [[AGXT2]], [[AGXT2L1]], [[AHSG]], [[AIF1]], [[AIFM3]], [[AK1]], [[AK2]], [[AK3]], [[AK3L1]], [[AK3L2]], [[AKAP1]], [[AKAP10]], [[AKR1B10]], [[AKR1C1]], [[AKR1C2]], [[AKR1C3]], [[AKR1C4]], [[AKR1D1]], [[AKT1]], [[ALAS1]], [[ALAS2]], [[ALDH18A1]], [[ALDH1A3]], [[ALDH1B1]], [[ALDH2]], [[ALDH3A2]], [[ALDH3B1]], [[ALDH3B2]], [[ALDH4A1]], [[ALDH5A1]], [[ALDH6A1]], [[ALDH7A1]], [[ALDH8A1]], [[ALDOA]], [[ALDOC]], [[ALG1]], [[ALG13]], [[ALOX12]], [[ALOX12B]], [[ALOX15]], [[ALOX15B]], [[ALOX5]], [[ALOX5AP]], [[ALOXE3]], [[ALPL]], [[ALS2]], [[AMACR]], [[AMBN]], [[AMDHD1]], [[AMELX]], [[AMELY]], [[AMID]], [[AMT]], [[ANG]], [[ANGPTL7]], [[ANKH]], [[ANKRD2]], [[ANKRD23]], [[ANKRD39]], [[ANXA1]], [[ANXA10]], [[ANXA8L2]], [[AOAH]], [[AOC3]], [[AOX1]], [[AP2M1]], [[APC]], [[APC2]], [[APLP1]], [[APOA2]], [[APOA5]], [[APOB48R ]], [[APOBEC1]], [[APOC1]], [[APOC3]], [[APOD]], [[APOF]], [[APOL1]], [[APOL2]], [[APOL3]], [[APOL5]], [[APOM]], [[APP]], [[ARAF]], [[ARG1]], [[ARG2]], [[ARHGEF11]], [[ARR3]], [[ARSA]], [[ART4]], [[ARV1]], [[ASAH1]], [[ASAH2]], [[ASAH3]], [[ASAH3L]], [[ASL]], [[ASNS]], [[ASNSD1]], [[ASPA]], [[ASPH]], [[ASPN]], [[ASS1]], [[ATBF1]], [[ATF4]], [[ATOX1]], [[ATP1A2]], [[ATP2A1]], [[ATP5A1]], [[ATP5B]], [[ATP5C1]], [[ATP5D]], [[ATP5E]], [[ATP5F1]], [[ATP5G1]], [[ATP5G2]], [[ATP5G3]], [[ATP5H]], [[ATP5I]], [[ATP5J]], [[ATP5J2]], [[ATP5L]], [[ATP5O]], [[ATP5S]], [[ATP6V0A4]], [[ATP6V1A]], [[ATP6V1B1]], [[ATP6V1E1]], [[ATP7A]], [[ATP8B1]], [[ATP8B3]], [[ATPAF1]], [[ATPAF2]], [[ATRN]], [[AUH]], [[AXIN1]], [[AXIN2]], [[AYTL1]], [[AYTL2]], [[AZGP1]], [[B3GALT1]], [[B3GNT5]], [[B4GALNT1]], [[B4GALNT2]], [[B4GALT4]], [[BAAT]], [[BAD]], [[BARX1]], [[BARX2]], [[BAX]], [[BBC3]], [[BBS4]], [[BCAT1]], [[BCAT2]], [[BCDO2]], [[BCKDHA]], [[BCKDHB]], [[BCKDK]], [[BCL2]], [[BCL2L1]], [[BCL2L10]], [[BCL2L13]], [[BCL2L2]], [[BCL6]], [[BCL9]], [[BCS1L]], [[BDH1]], [[BDH2]], [[BDKRB1]], [[BDKRB2]], [[BGLAP]], [[BGN]], [[BHMT]], [[BID]], [[BIK]], [[BLNK]], [[BMP1]], [[BMP2]], [[BMP3]], [[BMP4]], [[BMP5]], [[BMP6]], [[BMP7]], [[BMP8A]], [[BMP8B]], [[BMPR1B]], [[BNIP3]], [[BNIP3L]], [[BPHL]], [[BRCA1]], [[BRD7]], [[BRP44]], [[BRP44L]], [[BRS3]], [[BRUNOL6]], [[BTG1]], [[BTN2A1]], [[BTN3A1]], [[BTNL3]], [[BTRC]], [[BVES]], [[BZRAP1]], [[C10orf10]], [[C10orf33]], [[C10orf65]], [[C11orf11]], [[C14orf1]], [[C14orf112]], [[C14orf126]], [[C14orf148]], [[C14orf156]], [[C14orf159]], [[C14orf2]], [[C14orf21]], [[C18orf22]], [[C18orf55]], [[C1orf166]], [[C1orf31]], [[C1orf69]], [[C1QBP]], [[C1QDC1]], [[C1QTNF2]], [[C1QTNF3]], [[C21orf33]], [[C2orf25]], [[C3]], [[C3AR1]], [[C3orf1]], [[C3orf15]], [[C3orf23]], [[C3orf31]], [[C4A]], [[C4B]], [[C4orf14]], [[C5]], [[C5orf33]], [[C6]], [[C7]], [[C8A]], [[C8B]], [[C8G]], [[C8orf61]], [[C9]], [[C9orf4]], [[CA5A]], [[CA5B]], [[CABC1]], [[CACNA1H]], [[CACNA1S]], [[CACNB1]], [[CACNB2]], [[CACNG1]], [[CAD]], [[CALCA]], [[CALCR]], [[CALCRL]], [[CALD1]], [[CAPN3]], [[CARD12]], [[CARD4]], [[CARS]], [[CARTPT]], [[CASP7]], [[CASP8]], [[CASQ1]], [[CASQ2]], [[CASR]], [[CAT]], [[CAV3]], [[CBFB]], [[CBS]], [[CCDC19]], [[CCDC39]], [[CCDC44]], [[CCDC56]], [[CCDC90B]], [[CCKAR]], [[CCL1]], [[CCL11]], [[CCL13]], [[CCL16]], [[CCL17]], [[CCL18]], [[CCL19]], [[CCL2]], [[CCL20]], [[CCL21]], [[CCL22]], [[CCL23]], [[CCL24]], [[CCL25]], [[CCL26]], [[CCL3]], [[CCL3L1]], [[CCL4]], [[CCL4L1]], [[CCL5]], [[CCL7]], [[CCL8]], [[CCR1]], [[CCR2]], [[CCR3]], [[CCR4]], [[CCR5]], [[CCR7]], [[CD14]], [[CD163]], [[CD180]], [[CD248]], [[CD276]], [[CD3E]], [[CD4]], [[CD74]], [[CD80]], [[CD81]], [[CD93]], [[CD97]], [[CDH11]], [[CDIPT]], [[CDK5]], [[CDO1]], [[CDON]], [[CDS1]], [[CDS2]], [[CEBPB]], [[CEECAM1]], [[CEL]], [[CEPT1]], [[CERK]], [[CETP]], [[CH25H]], [[CHAD]], [[CHAT]], [[CHCHD3]], [[CHCHD4]], [[CHDH]], [[CHI3L1]], [[CHKA]], [[CHKB]], [[CHL1]], [[CHODL]], [[CHPT1]], [[CHRD]], [[CHRDL1]], [[CHRDL2]], [[CHRM3]], [[CHRNA1]], [[CHRNB1]], [[CHRND]], [[CHRNE]], [[CHRNG]], [[CHST1]], [[CHST2]], [[CHST4]], [[CIAS1]], [[CIDEA]], [[CILP]], [[CILP2]], [[CKB]], [[CKLF]], [[CKMT1A]], [[CKMT1B]], [[CKMT2]], [[CLC]], [[CLCA1]], [[CLCF1]], [[CLCN1]], [[CLDN15]], [[CLEC3A]], [[CLIC1]], [[CLIC4]], [[CLN3]], [[CLN6]], [[CLN8]], [[CLPP]], [[CLPS]], [[CLPX]], [[CLTC]], [[CLU]], [[CMAS]], [[CNN1]], [[CNN3]], [[COG8]], [[COL10A1]], [[COL11A1]], [[COL11A2]], [[COL12A1]], [[COL13A1]], [[COL14A1]], [[COL16A1]], [[COL17A1]], [[COL19A1]], [[COL1A1]], [[COL1A2]], [[COL20A1]], [[COL23A1]], [[COL24A1]], [[COL27A1]], [[COL2A1]], [[COL4A1]], [[COL4A2]], [[COL4A4]], [[COL4A5]], [[COL4A6]], [[COL5A1]], [[COL5A2]], [[COL5A3]], [[COL6A1]], [[COL6A2]], [[COL6A3]], [[COL7A1]], [[COL8A1]], [[COL8A2]], [[COL9A1]], [[COL9A2]], [[COL9A3]], [[COLQ]], [[COMMD8]], [[COMP]], [[COQ10A]], [[COQ10B]], [[COQ2]], [[COQ3]], [[COQ4]], [[COQ5]], [[COQ6]], [[COQ7]], [[COQ9]], [[CORO2A]], [[COX10]], [[COX11]], [[COX15]], [[COX17]], [[COX18]], [[COX4I1]], [[COX4I2]], [[COX4NB]], [[COX5A]], [[COX5B]], [[COX6A1]], [[COX6A2]], [[COX6B1]], [[COX6BP3]], [[COX6C]], [[COX7A1]], [[COX7A2]], [[COX7A2L]], [[COX7AP2]], [[COX7B]], [[COX7B2]], [[COX7C]], [[COX8A]], [[COX8C]], [[CPNE1]], [[CPNE3]], [[CPNE6]], [[CPNE7]], [[CPOX]], [[CPS1]], [[CPT1A]], [[CPT1B]], [[CPT1C]], [[CPT2]], [[CPZ]], [[CRAT]], [[CREBL1]], [[CRISP3]], [[CRLS1]], [[CROT]], [[CRP]], [[CRTAP]], [[CRY1]], [[CRYAB]], [[CRYL1]], [[CS]], [[CSF1]], [[CSF3R]], [[CSK2B]], [[CSNK1A1]], [[CSNK1A1L]], [[CSNK1D]], [[CSNK1G1]], [[CSNK1G2]], [[CSNK1G3]], [[CSNK2A1]], [[CSNK2A2]], [[CSNK2B]], [[CSPG2]], [[CSRP2]], [[CSRP3]], [[CTBP1]], [[CTBP2]], [[CTF1]], [[CTGF]], [[CTH]], [[CTHRC1]], [[CTNNB1]], [[CTNNBIP1]], [[CTNND1]], [[CTNS]], [[CTPS]], [[CTPS2]], [[CTSB]], [[CTSD]], [[CUBN]], [[CUGBP2]], [[CX3CL1]], [[CXADR]], [[CXCL1]], [[CXCL10]], [[CXCL11]], [[CXCL13]], [[CXCL14]], [[CXCL16]], [[CXCL2]], [[CXCL3]], [[CXCL5]], [[CXCL6]], [[CXCL9]], [[CXorf20]], [[CXXC4]], [[CYB5A]], [[CYB5B]], [[CYBA]], [[CYBB]], [[CYC1]], [[CYCS]], [[CYP11A1]], [[CYP11B1]], [[CYP17A1]], [[CYP19A1]], [[CYP21A2]], [[CYP24A1]], [[CYP27A1]], [[CYP27B1]], [[CYP39A1]], [[CYP3A4]], [[CYP3A5]], [[CYP46A1]], [[CYP4A11]], [[CYP4F11]], [[CYP4F2]], [[CYP4F3]], [[CYP4F8]], [[CYP51A1]], [[CYP7A1]], [[CYP7B1]], [[D2HGDH]], [[DACT1]], [[DAG1]], [[DALRD3]], [[DAP3]], [[DARS]], [[DARS2]], [[DBH]], [[DBT]], [[DCBLD2]], [[DCI]], [[DCN]], [[DCT]], [[DCTN6]], [[DDAH1]], [[DDAH2]], [[DDHD1]], [[DDO]], [[DDT]], [[DDX28]], [[DECR1]], [[DEGS1]], [[DEGS2]], [[DES]], [[DGAT1]], [[DGAT2]], [[DGAT2L3]], [[DGAT2L4]], [[DGAT2L6]], [[DGCR6]], [[DGKD]], [[DGKE]], [[DGKK]], [[DGUOK]], [[DHCR24]], [[DHFR]], [[DHFRL1]], [[DHFRP1]], [[DHODH]], [[DHRS1]], [[DHRS2]], [[DHRS3]], [[DHRS4]], [[DHRS8]], [[DHRS9]], [[DIABLO]], [[DIXDC1]], [[DKK1]], [[DKK2]], [[DKK3]], [[DKK4]], [[DLAT]], [[DLD]], [[DLST]], [[DLSTP]], [[DMBT1]], [[DMD]], [[DMGDH]], [[DMP1]], [[DMPK]], [[DNAJA3]], [[DNAJC11]], [[DNAJC19]], [[DNAJC9]], [[DNER]], [[DNM3]], [[DOCK2]], [[DOK7]], [[DPAGT1]], [[DPM1]], [[DPM2]], [[DPM3]], [[DPT]], [[DPYSL2]], [[DSP]], [[DSPG3]], [[DSPP]], [[DST]], [[DTNA]], [[DUOX1]], [[DUOX2]], [[DUSP1]], [[DUT]], [[DVL1]], [[DYRK1B]], [[DYSF]], [[EARS2]], [[EBP]], [[EBPL]], [[ECH1]], [[ECHDC3]], [[ECHS1]], [[ECM1]], [[ECM2]], [[EDF1]], [[EDG3]], [[EDN1]], [[EDN2]], [[EDNRA]], [[EFEMP1]], [[EFHD1]], [[EGF]], [[EGFR]], [[EGR3]], [[EHHADH]], [[EIF2AK3]], [[EIF2AK4]], [[ELA2]], [[ELA3A]], [[ELA3B]], [[ELN]], [[ELOVL1]], [[ELOVL2]], [[ELOVL3]], [[ELOVL4]], [[ELOVL6]], [[EMD]], [[EMID1]], [[EMID2]], [[EMILIN1]], [[EMILIN2]], [[EMILIN3]], [[EMILIN3]], [[ENAM]], [[ENDOG]], [[ENPP1]], [[ENPP6]], [[ENPP7]], [[EP300]], [[EPRS]], [[EPX]], [[ERBB2IP]], [[ERCC2]], [[EREG]], [[ESR2]], [[ETFA]], [[ETFB]], [[ETFDH]], [[ETHE1]], [[ETNK1]], [[EVC]], [[EZH2]], [[F11R]], [[FAAH]], [[FABP1]], [[FABP2]], [[FABP4]], [[FABP5]], [[FABP6]], [[FABP7]], [[FADS1]], [[FADS2]], [[FADS3]], [[FAH]], [[FAHD1]], [[FAM121A]], [[FARS2]], [[FARSLA]], [[FARSLB]], [[FASN]], [[FBLN1]], [[FBLN2]], [[FBN2]], [[FBN3]], [[FBXW11]], [[FBXW4]], [[FCER1A]], [[FCER1G]], [[FCMD]], [[FDFT1]], [[FDPS]], [[FDX1]], [[FDXR]], [[FECH]], [[FER1L3]], [[FGF18]], [[FGF2]], [[FGF23]], [[FGFR2]], [[FGFR3]], [[FH]], [[FHL1]], [[FHL3]], [[FIBP]], [[FIS1]], [[FKBP1B]], [[FKBP8]], [[FLII]], [[FLJ12118]], [[FLNB]], [[FLRT1]], [[FLRT2]], [[FLRT3]], [[FMOD]], [[FN1]], [[FNTB]], [[FOS]], [[FOXC1]], [[FOXRED1]], [[FPGS]], [[FPR1]], [[FPRL1]], [[FRAS1]], [[FRAT1]], [[FRAT2]], [[FREM1]], [[FREM2]], [[FREM3]], [[FRRS1]], [[FRZB]], [[FTCD]], [[FTMT]], [[FUT10]], [[FXC1]], [[FXN]], [[FXR1]], [[FXYD1]], [[FZD1]], [[FZD10]], [[FZD2]], [[FZD3]], [[FZD4]], [[FZD5]], [[FZD6]], [[FZD7]], [[FZD8]], [[FZD9]], [[GAB1]], [[GAD1]], [[GAD2]], [[GAL]], [[GAL3ST1]], [[GAL3ST4]], [[GALC]], [[GALR2]], [[GAMT]], [[GANC]], [[GARS]], [[GAST]], [[GATA6]], [[GATM]], [[GBA]], [[GBA2]], [[GBAP]], [[GBAS]], [[GBGT1]], [[GCAT]], [[GCDH]], [[GCH1]], [[GCK]], [[GCLM]], [[GCSH]], [[GDF8]], [[GFER]], [[GFM1]], [[GFM2]], [[GFPT1]], [[GFPT2]], [[GGH]], [[GGPS1]], [[GGT1]], [[GGTLA1]], [[GHITM]], [[GIMAP5]], [[GIYD1]], [[GIYD2]], [[GJA1]], [[GJA10]], [[GJA5]], [[GJA7]], [[GK]], [[GK2]], [[GLA]], [[GLDC]], [[GLMN]], [[GLOXD1]], [[GLRX2]], [[GLRX5]], [[GLS]], [[GLS2]], [[GLT25D1]], [[GLT25D2]], [[GLUD1]], [[GLUD2]], [[GLUL]], [[GLULD1]], [[GLYAT]], [[GM2A]], [[GMPS]], [[GNAO1]], [[GNE]], [[GNPAT]], [[GOT1]], [[GOT1L1]], [[GOT2]], [[GPAA1]], [[GPAM]], [[GPC1]], [[GPC2]], [[GPC3]], [[GPC4]], [[GPC5]], [[GPC6]], [[GPD2]], [[GPHN]], [[GPLD1]], [[GPR175]], [[GPR68]], [[GPRC5C]], [[GPX1]], [[GPX2]], [[GPX3]], [[GPX4]], [[GPX5]], [[GPX6]], [[GPX7]], [[GRHL3]], [[GRHPR]], [[GRN]], [[GRPEL1]], [[GRPEL2]], [[GSK3B]], [[GSR]], [[GSS]], [[GSTZ1]], [[GTF2H4]], [[GYLTL1B]], [[HACL1]], [[HADH]], [[HADH2]], [[HADHA]], [[HADHB]], [[HAL]], [[HAO1]], [[HAO2]], [[HAPLN1]], [[HAPLN2]], [[HAPLN3]], [[HAPLN4]], [[HARS]], [[HARS2]], [[HARSL]], [[HAS1]], [[HAX1]], [[HBEGF]], [[HBLD2]], [[HBP1]], [[HCCS]], [[HCLS1]], [[HCN2]], [[HCN4]], [[HDAC4]], [[HDAC5]], [[HDAC7A]], [[HDAC9]], [[HDC]], [[HDHD3]], [[HDLBP]], [[HEBP1]], [[HEXA]], [[HEXB]], [[HGD]], [[HIBADH]], [[HINT2]], [[HK1]], [[HK2]], [[HMG20B]], [[HMGCL]], [[HMGCR]], [[HMGCS1]], [[HMGCS2]], [[HOXA3]], [[HPD]], [[HPGD]], [[HPSE]], [[HRC]], [[HRH1]], [[HRNR]], [[HSCB]], [[HSD11B1]], [[HSD11B2]], [[HSD17B1]], [[HSD17B12]], [[HSD17B2]], [[HSD17B3]], [[HSD17B4]], [[HSD17B6]], [[HSD17B7]], [[HSD17B8]], [[HSD3B1]], [[HSD3B2]], [[HSD3B7]], [[HSDL2]], [[HSP90AB1]], [[HSPA1A]], [[HSPA1B]], [[HSPA2]], [[HSPA9]], [[HSPB2]], [[HSPD1]], [[HSPE1]], [[HSPG2]], [[HTN1]], [[HTN3]], [[HTRA2]], [[IARS]], [[IARS2]], [[IBSP]], [[ID2B]], [[IDH1]], [[IDH2]], [[IDH3A]], [[IDH3B]], [[IDH3G]], [[IDI1]], [[IDI2]], [[IFI6]], [[IFNA2]], [[IFNG]], [[IFRD1]], [[IGF1]], [[IGFBP3]], [[IGSF8]], [[IHH]], [[IHPK3]], [[IL10]], [[IL13]], [[IL16]], [[IL17A]], [[IL17B]], [[IL17C]], [[IL17D]], [[IL18RAP]], [[IL1A]], [[IL1B]], [[IL1F10]], [[IL1F5]], [[IL1F6]], [[IL1R1]], [[IL1RAP]], [[IL1RN]], [[IL2]], [[IL20]], [[IL22]], [[IL22RA2]], [[IL23A]], [[IL25]], [[IL29]], [[IL2RA]], [[IL3]], [[IL31RA]], [[IL4]], [[IL4I1]], [[IL5]], [[IL7]], [[IL8RA]], [[IL8RB]], [[IL9]], [[IMMP1L]], [[IMMP2L]], [[IMMT]], [[IMPA1]], [[IMPACT]], [[IMPG1]], [[IMPG2]], [[INDO]], [[INPP5E]], [[INVS]], [[IRAK2]], [[IRF7]], [[ISCU]], [[ISOC2]], [[ISYNA1]], [[ITCH]], [[ITGA1]], [[ITGA11]], [[ITGA2]], [[ITGA4]], [[ITGA7]], [[ITGAL]], [[ITGAM]], [[ITGB1]], [[ITGB1BP2]], [[ITGB1BP3]], [[ITGB2]], [[ITGB6]], [[IVD]], [[JAG1]], [[JPH1]], [[JUB]], [[KAL1]], [[KARS]], [[KAZALD1]], [[KBTBD10]], [[KCNA1]], [[KCNB2]], [[KCNE1]], [[KCNE2]], [[KCNH1]], [[KCNH2]], [[KCNJ12]], [[KCNMA1]], [[KCNMB1]], [[KCNMB2]], [[KCNQ1]], [[KERA]], [[KIAA0101]], [[KIAA0141]], [[KIAA0564]], [[KIAA0564]], [[KIAA1683]], [[KIAA1967]], [[KIF1B]], [[KITLG]], [[KL]], [[KLF10]], [[KLHL12]], [[KLK6]], [[KLRG1]], [[KMO]], [[KNG1]], [[KRAS]], [[KREMEN1]], [[KREMEN2]], [[KRT19]], [[KYNU]], [[L2HGDH]], [[LACTB2]], [[LAD1]], [[LAMA1]], [[LAMA2]], [[LAMA3]], [[LAMA5]], [[LAMB1]], [[LAMB2]], [[LAMB3]], [[LAMB4]], [[LAMC1]], [[LAMC2]], [[LAMC3]], [[LAP3]], [[LARGE]], [[LARS]], [[LARS2]], [[LASS2]], [[LASS3]], [[LASS4]], [[LASS5]], [[LASS6]], [[LCE3A]], [[LCE3B]], [[LCN12]], [[LCN6]], [[LDB1]], [[LDHD]], [[LDLR]], [[LDLRAP1]], [[LECT1]], [[LEF1]], [[LEP]], [[LETM1]], [[LGALS1]], [[LGALS12]], [[LGALS13]], [[LGALS3]], [[LGALS3BP]], [[LIAS]], [[LIF]], [[LIPA]], [[LIPC]], [[LIPE]], [[LIPF]], [[LIPG]], [[LIPH]], [[LIPI]], [[LIPJ]], [[LIPK]], [[LIPL3]], [[LIPN]], [[LIPT1]], [[LOC493869]], [[LONP1]], [[LOX]], [[LPGAT1]], [[LPIN1]], [[LPO]], [[LRP1]], [[LRP10]], [[LRP16 ]], [[LRP2]], [[LRP4]], [[LRP5]], [[LRP6]], [[LRP8]], [[LRPPRC]], [[LRRC10]], [[LRRFIP2]], [[LSS]], [[LTA4H]], [[LTB4DH]], [[LTB4R]], [[LTB4R2]], [[LTBP1]], [[LTBP2]], [[LTBP4]], [[LTC4S]], [[LUC7L]], [[LUM]], [[LY6G5B]], [[LY75]], [[LY86]], [[LY96]], [[LYN]], [[LYPLA1]], [[LYPLA2]], [[LYPLA3]], [[MAGEE1]], [[Magmas]], [[MAML1]], [[MAOA]], [[MAOB]], [[MAP1D]], [[MAP2K3]], [[MAP2K3]], [[MAP3K1]], [[MAPK12]], [[MAPK14]], [[MAPK8]], [[MARS]], [[MARS2]], [[MASA]], [[MAT1A]], [[MAT2A]], [[MAT2B]], [[MATN1]], [[MATN2]], [[MATN3]], [[MATN4]], [[MBL2]], [[MBNL1]], [[MBNL3]], [[MBTPS1]], [[MBTPS2]], [[MC1R]], [[MCART1]], [[MCAT]], [[MCCC1]], [[MCCC2]], [[MCCD1]], [[MCEE]], [[MCL1]], [[MDH2]], [[ME2]], [[ME3]], [[MECR]], [[MEF2A]], [[MEF2B]], [[MEF2C]], [[MEF2D]], [[MEFV]], [[MEPE]], [[MET]], [[METTL8]], [[MFAP1]], [[MFAP2]], [[MFAP3]], [[MFAP4]], [[MFAP5]], [[MFN1]], [[MFN2]], [[MGC26963]], [[MGLL]], [[MGP]], [[MGST1]], [[MGST2]], [[MGST3]], [[MIF]], [[MINPP1]], [[MIPEP]], [[MIR16]], [[MITF]], [[MKL2]], [[MKX]], [[MLLT7]], [[MLNR]], [[MLYCD]], [[MMAA]], [[MMAB]], [[MMP1]], [[MMP10]], [[MMP11]], [[MMP12]], [[MMP13]], [[MMP14]], [[MMP15]], [[MMP16]], [[MMP17]], [[MMP2]], [[MMP20]], [[MMP21]], [[MMP23A]], [[MMP23B]], [[MMP24]], [[MMP25]], [[MMP26]], [[MMP27]], [[MMP28]], [[MMP3]], [[MMP7]], [[MMP8]], [[MMP9]], [[MMRN2]], [[MOBP]], [[MOGAT1]], [[MOGAT2]], [[MOGAT3]], [[MON2]], [[MOSC1]], [[MOSC2]], [[MOV10L1]], [[MOXD1]], [[MPO]], [[MPST]], [[MPV17]], [[MRAS]], [[MRP63]], [[MRPL1]], [[MRPL11]], [[MRPL12]], [[MRPL13]], [[MRPL14]], [[MRPL15]], [[MRPL16]], [[MRPL17]], [[MRPL18]], [[MRPL19]], [[MRPL20]], [[MRPL21]], [[MRPL23]], [[MRPL27]], [[MRPL28]], [[MRPL3]], [[MRPL32]], [[MRPL33]], [[MRPL34]], [[MRPL35]], [[MRPL36]], [[MRPL37]], [[MRPL39]], [[MRPL4]], [[MRPL40]], [[MRPL42]], [[MRPL43]], [[MRPL44]], [[MRPL45]], [[MRPL46]], [[MRPL47]], [[MRPL49]], [[MRPL50]], [[MRPL51]], [[MRPL9]], [[MRPS10]], [[MRPS11]], [[MRPS12]], [[MRPS14]], [[MRPS15]], [[MRPS16]], [[MRPS17]], [[MRPS18A]], [[MRPS18B]], [[MRPS18C]], [[MRPS2]], [[MRPS21]], [[MRPS22]], [[MRPS23]], [[MRPS24]], [[MRPS25]], [[MRPS26]], [[MRPS27]], [[MRPS28]], [[MRPS30]], [[MRPS31]], [[MRPS33]], [[MRPS34]], [[MRPS35]], [[MRPS36]], [[MRPS5]], [[MRPS6]], [[MRPS9]], [[MRRF]], [[MRS2L]], [[MSRA]], [[MSRB2]], [[MSRB3]], [[MSX1]], [[MT-ATP6]], [[MT-ATP8]], [[MTCH1]], [[MTCH2]], [[MT-CO1]], [[MT-CO2]], [[MT-CO3]], [[MTCP1]], [[MT-CYB]], [[MTERF]], [[MTERFD1]], [[MTERFD3]], [[MTFMT]], [[MTFR1]], [[MTHFD1]], [[MTHFD2]], [[MTIF2]], [[MTL5]], [[MTM1]], [[MTMR1]], [[MTMR10]], [[MTMR11]], [[MTMR12]], [[MTMR2]], [[MTMR3]], [[MTMR4]], [[MTMR6]], [[MTMR7]], [[MTMR8]], [[MTMR9]], [[MT-ND1]], [[MT-ND2]], [[MT-ND3]], [[MT-ND4]], [[MT-ND4L]], [[MT-ND5]], [[MT-ND6]], [[MTO1]], [[MTP18]], [[MTPN]], [[MTR]], [[MTRF1]], [[MTRF1L]], [[MTRR]], [[MTSS1]], [[MTTP]], [[MTX1]], [[MTX2]], [[MUC2]], [[MUC4]], [[MUC5AC]], [[MULK]], [[MUSK]], [[MUT]], [[MVD]], [[MVK]], [[MYBPC1]], [[MYBPC2]], [[MYBPC3]], [[MYBPH]], [[MYCBP]], [[MYD88]], [[MYEF2]], [[MYF5]], [[MYF6]], [[MYH1]], [[MYH10]], [[MYH11]], [[MYH13]], [[MYH2]], [[MYH3]], [[MYH4]], [[MYH6]], [[MYH7]], [[MYH8]], [[MYL1]], [[MYL2]], [[MYL3]], [[MYL4]], [[MYL6]], [[MYL6B]], [[MYL7]], [[MYL9]], [[MYLC2PL]], [[MYO5A]], [[MYOCD]], [[MYOD1]], [[MYOG]], [[MYOM1]], [[MYOM2]], [[MYOT]], [[MYOZ1]], [[NAB1]], [[NAB2]], [[NAGS]], [[NALP12]], [[NANS]], [[NAPG]], [[NARS]], [[NARS2]], [[NCDN]], [[NCR3]], [[NDST1]], [[NDUFA1]], [[NDUFA10]], [[NDUFA11]], [[NDUFA12]], [[NDUFA12L]], [[NDUFA13]], [[NDUFA2]], [[NDUFA3]], [[NDUFA4]], [[NDUFA5]], [[NDUFA6]], [[NDUFA7]], [[NDUFA8]], [[NDUFA9]], [[NDUFAB1]], [[NDUFAF1]], [[NDUFB1]], [[NDUFB10]], [[NDUFB11]], [[NDUFB2]], [[NDUFB3]], [[NDUFB4]], [[NDUFB5]], [[NDUFB6]], [[NDUFB7]], [[NDUFB8]], [[NDUFB9]], [[NDUFC1]], [[NDUFC2]], [[NDUFS1]], [[NDUFS2]], [[NDUFS3]], [[NDUFS4]], [[NDUFS5]], [[NDUFS6]], [[NDUFS7]], [[NDUFS8]], [[NDUFV1]], [[NDUFV2]], [[NDUFV3]], [[NEB]], [[NEFH]], [[NEO1]], [[NEU3]], [[NFAM1]], [[NFE2L1]], [[NFKB1]], [[NFKBIZ]], [[NFRKB]], [[NFS1]], [[NFX1]], [[NID1]], [[NID2]], [[NINJ1]], [[NINJ2]], [[NIPSNAP1]], [[NIT2]], [[NKX2-5]], [[NLK]], [[NLN]], [[NME4]], [[NME5]], [[NMI]], [[NMS]], [[NMU]], [[NMUR1]], [[NMUR2]], [[NNT]], [[NOL3]], [[NOS1]], [[NOS2A]], [[NOS3]], [[NOTCH1]], [[NOTCH2]], [[NOX4]], [[N-PAC]], [[NPC1]], [[NPC1L1]], [[NPC2]], [[NPHP3]], [[NPHS1]], [[NPNT]], [[NQO1]], [[NR0B1]], [[NR0B2]], [[NR1H2]], [[NR1H3]], [[NR1H4]], [[NR1I2]], [[NR2F2]], [[NR3C1]], [[NR5A1]], [[NR5A2]], [[NRD1]], [[NRG1]], [[NRIP1]], [[NSDHL]], [[NSMAF]], [[NT5M]], [[NTF3]], [[NTHL1]], [[NTN1]], [[NTN2L]], [[NTN4]], [[NTNG1]], [[NTNG2]], [[NTRK3]], [[NUDT1]], [[NUDT17]], [[NUDT8]], [[NUDT9]], [[NUP62]], [[NUP85]], [[NYX]], [[OAT]], [[OC90]], [[OCIAD2]], [[OCRL]], [[ODAM]], [[OGDH]], [[OGG1]], [[OGN]], [[OLAH]], [[OMD]], [[OPA1]], [[OPA3]], [[OPRS1]], [[OPTC]], [[ORM1]], [[OSBP]], [[OSBP2]], [[OSBPL10]], [[OSBPL11]], [[OSBPL1A]], [[OSBPL2]], [[OSBPL3]], [[OSBPL5]], [[OSBPL6]], [[OSBPL7]], [[OSBPL8]], [[OSBPL9]], [[OSTF1]], [[OSTN]], [[OTC]], [[OTOA]], [[OTOG]], [[OXA1L]], [[OXCT1]], [[OXCT2]], [[OXR1]], [[OXSM]], [[OXSR1]], [[OXTR]], [[P2RX5]], [[P2RX7]], [[P2RXL1]], [[P53AIP1]], [[PABPN1]], [[PACS2]], [[PAFAH1B1]], [[PAFAH1B2]], [[PAFAH1B3]], [[PAFAH2]], [[PAH]], [[PAK7]], [[PANK2]], [[PAPD1]], [[PARK7]], [[PARL]], [[PARP4]], [[PARS2]], [[PATE ]], [[PAX3]], [[PBX1]], [[PC]], [[PCCA]], [[PCCB]], [[PCK1]], [[PCK2]], [[PCSK9]], [[PCTP]], [[PCYT1A]], [[PCYT1B]], [[PCYT2]], [[PDCD8]], [[PDE3A]], [[PDE4D]], [[PDF]], [[PDGFB]], [[PDGFC]], [[PDGFD]], [[PDGFRB]], [[PDHA1]], [[PDHA2]], [[PDHB]], [[PDHX]], [[PDK1]], [[PDK2]], [[PDK3]], [[PDK4]], [[PDLIM1]], [[PDLIM7]], [[PDP2]], [[PDSS1]], [[PDSS2]], [[PECAM1]], [[PECI]], [[PECR]], [[PELO]], [[PEMT]], [[PEO1]], [[PEPD]], [[PET112L]], [[PEX11B]], [[PEX7]], [[PFAS]], [[PGAM2]], [[PGDS ]], [[PGEA1]], [[PGS1]], [[PHB]], [[PHCA]], [[PHEX]], [[PHGDH]], [[PHYH]], [[PI3]], [[PI4KII]], [[PICK1]], [[PIGA]], [[PIGB]], [[PIGC]], [[PIGF]], [[PIGG]], [[PIGH]], [[PIGK]], [[PIGL]], [[PIGM]], [[PIGN]], [[PIGO]], [[PIGP]], [[PIGQ]], [[PIGS]], [[PIGT]], [[PIGU]], [[PIGV]], [[PIGW]], [[PIGX]], [[PIGY]], [[PIGZ]], [[PIK3C2A]], [[PIK3CB]], [[PIK3R1]], [[PIK4CA]], [[PIK4CB]], [[PIN4]], [[PINK1]], [[PIP3-E]], [[PIP5K1A]], [[PIP5K1B]], [[PIP5K1C]], [[PIP5K2A]], [[PIP5K2B]], [[PISD]], [[PITPNA]], [[PITPNB]], [[PITPNM1]], [[PITPNM3]], [[PITRM1]], [[PITX2]], [[PKM2]], [[PLA1A]], [[PLA2G10]], [[PLA2G12A]], [[PLA2G12B]], [[PLA2G1B]], [[PLA2G2A]], [[PLA2G2D]], [[PLA2G2E]], [[PLA2G2F]], [[PLA2G3]], [[PLA2G4A]], [[PLA2G4B]], [[PLA2G4C]], [[PLA2G4D]], [[PLA2G4E]], [[PLA2G4F]], [[PLA2G5]], [[PLA2G6]], [[PLA2G7]], [[PLAA]], [[PLB1]], [[PLCB1]], [[PLCB2]], [[PLCB3]], [[PLCB4]], [[PLCD1]], [[PLCD3]], [[PLCD4]], [[PLCE1]], [[PLCG1]], [[PLCG2]], [[PLCH1]], [[PLCH2]], [[PLCL1]], [[PLCL2]], [[PLCZ1]], [[PLD1]], [[PLD2]], [[PLG]], [[PLIN]], [[PLN]], [[PLOD1]], [[PLP1]], [[PLTP]], [[PMF1]], [[PMPCA]], [[PMPCB]], [[PMVK]], [[PNKP]], [[PNLIP]], [[PNLIPRP1]], [[PNLIPRP2]], [[PNLIPRP3]], [[PNPLA1]], [[PNPLA10P]], [[PNPLA2]], [[PNPLA3]], [[PNPLA4]], [[PNPLA5]], [[PNPLA7]], [[PNPLA8]], [[PNPT1]], [[POLDIP2]], [[POLG]], [[POLG2]], [[POLRMT]], [[PORCN]], [[POSTN]], [[POU6F1]], [[PPA2]], [[PPAP2A]], [[PPARA]], [[PPARD]], [[PPARG]], [[PPARGC1A]], [[PPAT]], [[PPGB]], [[PPIF]], [[PPM2C]], [[PPOX]], [[PPP1R12A]], [[PPP1R12B]], [[PPP1R15B]], [[PPP1R9B]], [[PPP2CA]], [[PPP2R1A]], [[PPP2R1B]], [[PPT1]], [[PRAM1]], [[PRDX2]], [[PRDX3]], [[PRDX4]], [[PRDX5]], [[PRDX6]], [[PRELP]], [[PRG2]], [[PRG3]], [[PRKAA1]], [[PRKAA2]], [[PRKAB1]], [[PRKAB2]], [[PRKACG]], [[PRKAG1]], [[PRKAG2]], [[PRKAG3]], [[PRKAR2B]], [[PRKCA]], [[PRKCE]], [[PRKG1]], [[PRLR]], [[PRNP]], [[PROCA1 ]], [[PRODH]], [[PRODH2]], [[PROK2]], [[PRSS36]], [[PRTG]], [[PSAP]], [[PSAPL1]], [[PSAT1]], [[PSMB5]], [[PSPH]], [[PTAFR]], [[PTDSS1]], [[PTDSS2]], [[PTEN]], [[PTGDS]], [[PTGER4]], [[PTGES]], [[PTGES2]], [[PTGES3]], [[PTGIS]], [[PTH]], [[PTHLH]], [[PTHR1]], [[PTHR2]], [[PTN]], [[PTOV1]], [[PTPMT1]], [[PTPRZ1]], [[PTRH2]], [[PTS]], [[PTX3]], [[PYCARD]], [[PYCR1]], [[PYCR2]], [[PYCRL]], [[PYGO1]], [[PYGO2]], [[QARS]], [[QDPR]], [[QKI]], [[RAB11FIP5]], [[RAB32]], [[RAF1]], [[RAI14]], [[RARRES2]], [[RARS]], [[RARSL]], [[RB1]], [[RBM12]], [[RBP1]], [[RBP3]], [[RDH11]], [[RDH12]], [[RDH16]], [[RDH8]], [[REEP1]], [[REG3A]], [[REG3G]], [[RELA]], [[RELN]], [[RETSAT]], [[REXO2]], [[RHOT1]], [[RHOT2]], [[RIPK2]], [[RNASE4]], [[RNASEH1]], [[RNF7]], [[ROBO2]], [[ROCK2]], [[ROR2]], [[RORA]], [[RPE65]], [[RPS27A]], [[RPTN]], [[RSPO1]], [[RSPO2]], [[RSPO3]], [[RSPO4]], [[RTN4IP1]], [[RTN4RL1]], [[RTN4RL2]], [[RUNX2]], [[RYR1]], [[RYR2]], [[S100A12]], [[S100A8]], [[S100A9]], [[SAMD8]], [[SAMM50]], [[SARDH]], [[SARS]], [[SARS2]], [[SBF1]], [[SBF2]], [[SC4MOL]], [[SC5DL]], [[SCAP ]], [[SCARA3]], [[SCARB1]], [[SCD]], [[SCD5]], [[SCLY]], [[SCN4A]], [[SCN5A]], [[SCN7A]], [[SCN8A]], [[SCO1]], [[SCO2]], [[SCP2]], [[SCRT2]], [[SCYE1]], [[SDHA]], [[SDHB]], [[SDHC]], [[SDHD]], [[SDS]], [[SDSL]], [[SEC14L2]], [[SELE]], [[SELI ]], [[SELP]], [[SELS]], [[SENP2]], [[SEPP1]], [[SEPT4]], [[SERINC1]], [[SERINC2]], [[SERINC5]], [[SERPINA3]], [[SFRP1]], [[SFRP2]], [[SFRP4]], [[SFRP5]], [[SFTPB]], [[SFTPD]], [[SFXN1]], [[SFXN2]], [[SFXN3]], [[SFXN4]], [[SFXN5]], [[SGCA]], [[SGCB]], [[SGCD]], [[SGCE]], [[SGCG]], [[SGCZ]], [[SGK2]], [[SGPL1]], [[SGPP1]], [[SH3BP5]], [[SH3GLB1]], [[SHANK3]], [[SHH]], [[SHMT1]], [[SHMT2]], [[SIGLEC1]], [[SILV]], [[SIRT1]], [[SIRT2]], [[SIRT3]], [[SIX1]], [[SIX3]], [[SIX4]], [[SLC25A1]], [[SLC25A10]], [[SLC25A11]], [[SLC25A12]], [[SLC25A13]], [[SLC25A14]], [[SLC25A15]], [[SLC25A16]], [[SLC25A17]], [[SLC25A18]], [[SLC25A19]], [[SLC25A2]], [[SLC25A20]], [[SLC25A21]], [[SLC25A22]], [[SLC25A23]], [[SLC25A24]], [[SLC25A25]], [[SLC25A26]], [[SLC25A27]], [[SLC25A28]], [[SLC25A29]], [[SLC25A3]], [[SLC25A30]], [[SLC25A31]], [[SLC25A32]], [[SLC25A33]], [[SLC25A35]], [[SLC25A36]], [[SLC25A37]], [[SLC25A38]], [[SLC25A39]], [[SLC25A4]], [[SLC25A40]], [[SLC25A41]], [[SLC25A42]], [[SLC25A43]], [[SLC25A44]], [[SLC25A45]], [[SLC25A5]], [[SLC25A6]], [[SLC27A1]], [[SLC27A2]], [[SLC27A3]], [[SLC27A4]], [[SLC27A5]], [[SLC27A6]], [[SLC35B3]], [[SLC3A1]], [[SLC45A2]], [[SLC5A3]], [[SLC6A14]], [[SLC6A6]], [[SLC6A8]], [[SLC7A1]], [[SLC7A2]], [[SLC7A4]], [[SLC7A5]], [[SLC7A6]], [[SLC7A7]], [[SLC7A8]], [[SLC7A9]], [[SLC8A1]], [[SLC9A3R1]], [[SLC9A6]], [[SLMAP]], [[SMAD3]], [[SMC3]], [[SMCP]], [[SMG1 ]], [[SMO]], [[SMOC1]], [[SMOC2]], [[SMPD1]], [[SMPD2]], [[SMPD3]], [[SMPX]], [[SMS]], [[SMTN]], [[SNCA]], [[SNCB]], [[SNTA1]], [[SNTB1]], [[SNTB2]], [[SNTG1]], [[SNTG2]], [[SOAT2]], [[SOCS1]], [[SOCS3]], [[SOD1]], [[SOD2]], [[SOD2]], [[SOD3]], [[SORL1]], [[SORT1]], [[SOST]], [[SOSTDC1]], [[SOX15]], [[SOX6]], [[SP7]], [[SPACA3]], [[SPARC]], [[SPARCL1]], [[SPATA19]], [[SPEG]], [[SPG7]], [[SPHK1]], [[SPHK2]], [[SPN]], [[SPOCK1]], [[SPOCK2]], [[SPOCK3]], [[SPON1]], [[SPON2]], [[SPP1]], [[SPP2]], [[SPRR3]], [[SPTLC1]], [[SQLE]], [[SQRDL]], [[SRD5A1]], [[SRD5A2]], [[SREBF1]], [[SREBF2]], [[SRF]], [[SRI]], [[SRPK3]], [[SRR]], [[SRXN1]], [[SSBP1]], [[SSPN]], [[ST3GAL5]], [[ST3GAL6]], [[ST6GALNAC4]], [[ST6GALNAC6]], [[ST8SIA1]], [[ST8SIA3]], [[ST8SIA5]], [[ST8SIA6]], [[STAR]], [[STARD3]], [[STARD4]], [[STARD5]], [[STAT5A]], [[STAT5B]], [[STATH]], [[STK25]], [[STOML2]], [[STS]], [[STXBP1]], [[SUCLA2]], [[SUCLG1]], [[SUCLG2]], [[SULT1A1]], [[SULT1A2]], [[SULT1A3]], [[SULT1B1]], [[SULT1E1]], [[SULT2A1]], [[SULT2B1]], [[SULT4A1]], [[SUMF1]], [[SUOX]], [[SUPV3L1]], [[SURF1]], [[SVIL]], [[SYK]], [[SYNE1]], [[SYNJ2BP]], [[SYT7]], [[TAC1]], [[TACR1]], [[TACR2]], [[TAF9]], [[TAGLN]], [[TAGLN2]], [[TAGLN3]], [[TARS]], [[TARSL1]], [[TARSL2]], [[TAT]], [[TAX1BP3]], [[TAZ]], [[TBC1D15]], [[TBRG4]], [[TBX1]], [[TBX18]], [[TBX20]], [[TBXA2R]], [[TCAP]], [[TCF1]], [[TCF12]], [[TCF7]], [[TCF7L1]], [[TCF7L2]], [[TDGF1]], [[TDGF3]], [[TDO2]], [[TEAD4]], [[TECTA]], [[TECTB]], [[TFAM]], [[TFCP2L1]], [[TFIP11]], [[TGFB1]], [[TGFB2]], [[TGFBI]], [[TGM2]], [[THBS2]], [[THBS3]], [[THBS4]], [[THEM2]], [[THG1L]], [[THNSL1]], [[THRA]], [[THRSP]], [[TIMM10]], [[TIMM13]], [[TIMM17A]], [[TIMM17B]], [[TIMM22]], [[TIMM23]], [[TIMM44]], [[TIMM50]], [[TIMM8A]], [[TIMM8B]], [[TIMM9]], [[TIMP1]], [[TIMP2]], [[TIMP3]], [[TIMP4]], [[TINAG]], [[TIRAP]], [[TK2]], [[TLE1]], [[TLE2]], [[TLE3]], [[TLE4]], [[TLE6]], [[TLR1]], [[TLR10]], [[TLR2]], [[TLR3]], [[TLR4]], [[TLR5]], [[TLR6]], [[TLR7]], [[TLR8]], [[TLR9]], [[TM6SF2]], [[TM7SF2]], [[TMEM126A]], [[TMEM143]], [[TMEM15]], [[TMEM23]], [[TMLHE]], [[TMOD1]], [[TMOD4]], [[TNC]], [[TNF]], [[TNFAIP6]], [[TNFRSF11A]], [[TNFRSF11B]], [[TNFRSF1A]], [[TNFRSF1B]], [[TNFSF11]], [[TNFSF4]], [[TNK2]], [[TNN]], [[TNNC2]], [[TNNI1]], [[TNNI2]], [[TNNI3]], [[TNNT1]], [[TNNT2]], [[TNNT3]], [[TNR]], [[TNXB]], [[TOB1]], [[TOLLIP]], [[TOMM20]], [[TOMM22]], [[TOMM34]], [[TOMM40]], [[TOMM40L]], [[TOMM7]], [[TOMM70A]], [[TOP1MT]], [[TP53]], [[TPH1]], [[TPH2]], [[TPI1]], [[TPM1]], [[TPM3]], [[TPO]], [[TPP1]], [[TPST1]], [[TRAF6]], [[TRAK1]], [[TRAP1]], [[TRDN]], [[TRERF1]], [[TRIAP1]], [[TRIT1]], [[TRMU]], [[TRNT1]], [[TSFM]], [[TSPO]], [[TST]], [[TTN]], [[TTPA]], [[TUBA1A]], [[TUBA6]], [[TUBB3]], [[TUFM]], [[TUFT1]], [[TUSC3]], [[TWF2]], [[TWIST1]], [[TWSG1]], [[TXN2]], [[TXNDC14]], [[TXNIP]], [[TYR]], [[TYRP1]], [[UACA]], [[UBA52]], [[UBB]], [[UBC]], [[UCP1]], [[UCP2]], [[UCP3]], [[UGCG]], [[UGT1A@]], [[UGT1A1]], [[UGT1A10]], [[UGT1A3]], [[UGT1A4]], [[UGT1A5]], [[UGT1A6]], [[UGT1A7]], [[UGT1A8]], [[UGT1A9]], [[UGT2B10]], [[UGT2B11]], [[UGT2B15]], [[UGT2B17]], [[UGT2B4]], [[UGT2B7]], [[UGT8]], [[UNC45A]], [[UNC45B]], [[UNG]], [[UNQ2541 ]], [[UNQ9438 ]], [[UQCR]], [[UQCRB]], [[UQCRC1]], [[UQCRC2]], [[UQCRFS1]], [[UQCRH]], [[UQCRQ]], [[UROC1]], [[USH2A]], [[UTRN]], [[UTS2]], [[VAMP1]], [[VAMP5]], [[VARS]], [[VDAC1]], [[VDAC2]], [[VDAC3]], [[VDAC4]], [[VGLL2]], [[VHL]], [[VIP]], [[VIPR1]], [[VISA]], [[VLDLR]], [[VPS45A]], [[VTN]], [[VWA1]], [[WARS]], [[WARS2]], [[WASF1]], [[WIF1]], [[WISP1]], [[WNT1]], [[WNT1]], [[WNT10A]], [[WNT10B]], [[WNT11]], [[WNT16]], [[WNT2]], [[WNT2B]], [[WNT3]], [[WNT3A]], [[WNT4]], [[WNT5A]], [[WNT5B]], [[WNT6]], [[WNT7A]], [[WNT7B]], [[WNT8A]], [[WNT8B]], [[WNT9A]], [[WNT9B]], [[WWOX]], [[WWTR1]], [[XCR1]], [[XPA]], [[XPNPEP3]], [[YARS]], [[YARS2]], [[YME1L1]], [[YWHAH]], [[YWHAZ]], [[ZBTB33]], [[ZCD1]], [[ZFP36]], [[ZNF202]], [[ZNF675]], [[ZP1]], [[ZP2]], [[ZP3]], [[ZP4]]<br />
<br />
<br />
<br />
----<br />
<br />
== Community Input Section ==<br />
<br />
'''Please use the area below to add genes not included in the list above but which are known to be associated with cardiovascular processes. Alternatively use the space on [[Priority Cardiovascular genes|Priority Cardiovascular Genes Page]] to suggest genes to be prioritised for annotation. Thank you.''' <br />
<br />
GATA3, GATA4, TBX5, K+ channel genes, NOS2B, NOS2C<br />
<br />
GWAS: SCL30A8, IDE-KIF11-HHEX cluster, EXt2-ALX4 cluster, CDKN2A, CDKN2B, CDKAL1, IGF2BP2, FTO, KNCJ11</div>Simonthttps://wiki.geneontology.org/index.php?title=GO_Advisors_Meeting&diff=5777GO Advisors Meeting2006-08-28T20:37:27Z<p>Simont: /* Aim of the meeting */</p>
<hr />
<div>== Aim of the meeting == <br />
The main focus of this meeting is to obtain our advisors views and perspectives on the work we have planned (i.e. the new proposal) and the approach we are taking to accomplish our aims. <br />
<br />
Please add items below that you think need to be presented. When possible, please put your request in priority rank order:<br />
<br />
'''''Utility for Biologists'''''<br />
<br />
The highest priority for the GOC identified by grant reviewers and others is to enhance the ability of non-informatics biologists to access the GO resources as part of their data analysis efforts. Some of the participants in the GO Consortium provide access to GO data analysis tools as part of their MOD resource. But the GO site itself does not support data analysis directly from the site. We do provide listing of tools, but have not seen it as part of our 'mission' to support a general tool [such as GO TermFinder, for example] as part of the GOC. Should we do so? Wouldn't this be analogous to provide a BLAST server? While the individual MODs have a role to play here, the GOC is seen by some to be behind in supporting the work of the bench biologist.<br />
<br />
* I think this should be given a high priority for discussion. In the AmiGO WG we've discussed adding simple tools (e.g. a cgi of map2slim) to AmiGO, but for some of the more complex tools e.g. microarray tools it's probably not worth developing our own as so many good tools already exist. But should we 'endorse' some of these existing tools? And then how could we have say in the direction they're developed? We already work fairly closely with some of these groups (Onto-Express, GoMiner).<br />
* Related to the list of tools, its great to have this long list but it makes it very hard for new users to know which to use and why. Some sort of critical review of features and suggested uses would be very handy. Selecting/Endorsing a 'best' tool in a given category (if there was/were clear winners) would also be really helpful to users but maybe more controversial if done by GOC vs some external author.<br />
** In reviewing the tools one would identify lists of essential and desirable features that 'good' GO tools should ideally possess. If the GOC could approve a set of core features that all 'endorsed' tools should have this might provide a way to influence future tool development by others. Tools that met or exceeded the feature set would get higher billing than ones which didnt, presumably driving non-compliant tools to meet these higher standards or go by the wayside (similar to OBO foundry driving the development of higher quality ontologies).<br />
<br />
'''''Utility for GO-Tool Developers'''''<br />
<br />
This is a note from a developer...<br />
"we are in the process of making improvements to our GO analysis tool, the<br />
Ontologizer, and I have noticed that one of the most time consuming<br />
aspects of the process seems to be finding good datasets with which to<br />
test new algorithms. I would guess that we are not entirely alone in this.<br />
I wonder if it would be a good idea for the GO community to make a<br />
repository of datasets for testing new algorithms and also for new users<br />
to learn the ropes. I would be thinking of lists of study sets (say<br />
differentially expressed genes) with corresponding population sets (say<br />
all genes on the chip) together with short biological and methods<br />
descriptions. Does such a repository already exist or does anyone have any<br />
tips?"<br />
<br />
'''''Should GO capture the context of activity'''''<br />
<br />
Is there a facility to construct GO annotations which would capture the context in which a given gene product is associated with (e.g.) a given function? Thus, for example, instead of annotating protein X to oxygen transport [function] one might annotate:<br />
<br />
<protein X in cell component Y> to oxygen transport [function'] <br />
<br />
For MGI, this information is captured for cell types, anatomy and target molecules, but it is not a GO-wide policy. MGI captures this information in structured notes. So, for example MGI curators can make an annotation for gene product X having some function in oxygen transport in a lung epithelial cell. The hope is that if X is also annotated to oxygen transporter activity in lung epithelial cell and plasma membrane of a lung epithelial cell, then we can draw a conclusion that X has the potential to execute a function of an oxygen transporter involved in oxygen transport in the plasma membrane of a lung epithelial cell. In the right spatio-temporal context, the function will be executed.<br />
<br />
<br />
'''''Encouraging community annotation'''''<br />
#How can we help community scientists to get credit for their GO work? Could we publish a short account of the work of individual content meetings with all experts having author credit? Could groups providing manual annotation of their own gene products of interest get a small publication giving an account of their contribution and of possible applications?<br />
<br />
'''''Annotation Tool'''''<br />
#Who is the target audience for the annotation tool?<br />
#How does the idea of an annual functional annotation tool bake-off sound to you? How would you approach it? Can it be used to keep orphaned genomes up-to-date?<br />
#Almost everyone agrees that the GO Consortium should develop an annotation tool, [but not all people since most groups do annotation within the context of their genome annotation stream] Once we begin asking questions about what the tool should do, it becomes clear that every group has very different ideas about what such a tool should do. Groups within the GO tend to advocate for the development of a tool that satisfies their own research efforts at the moment, because that is the immediate need as they understand it. Could the advisors suggest a way of determining which of these special-purpose applications are best for the GO user community ''as a whole'', so that we can decide how to focus our development efforts? What's the best way to encourage inter-group communication to foster collaboration on tools and minimize redundant development efforts? How can we decide whether specific, highly targeted annotation tools or general, lowest-common-denominator annotation tools would be most useful to our user community?<br />
<br />
== Agenda ==<br />
In order to meet our objectives, we need to present all of the material in the morning.<br />
The presentations will focus on the goals and progress of the Consortium and will reflect the new organization and management of the GOC developed through the process of writing the GO Consortium competitive renewal. The times noted here are expected to be divided between a short presentation and then focused discussion on the topic.<br />
<br />
<br />
** - 8:00AM: Introductions (picture on display and circle everyone)<br />
** - 8:10 AM: Overview of Grant Aims (Michael-20 minutes)<br />
** - 8:30 AM: Reference Genomes (Rex - 30 minutes)<br />
** - 9:00 AM: Ontology/Database Developments - Biological (Midori and David-30 minutes)<br />
** - 9:30 AM: Ontology Developments – Technical (Chris-30 minutes)<br />
** -10:00 AM: Break (15 min)<br />
** -10:15 AM: Emerging Genomes (Jen-20 minutes)<br />
** -10:35AM: User Advocacy including AmiGO (Eurie & Jane- 20 minutes)<br />
** -10:55AM: New management structure (Suzi- 20 minutes)<br />
** -11:15AM: Summary of issues we face: pink sheets and more (Judy- 20 minutes)<br />
** -11:35AM: Open Discussion (all)<br />
** -12:30PM – 1:30PM, working lunch for Advisors and GO-top<br />
<br />
** - 1:30PM - 3:00PM, Advisors powwow<br />
** - 3:00 PM - break<br />
** - 3:30PM - 5:00PM, feedback from Advisors<br />
** - 6:00PM dinner with everyone<br />
<br />
== Participants ==<br />
*GO representatives<br />
#Michael Ashburner<br />
#Judy Blake<br />
#Eurie Hong<br />
#Suzi Lewis<br />
#Rex Chisholm<br />
#Jen Clark<br />
#Midori Harris<br />
#David Hill<br />
#Ben Hitz (representing production services)<br />
#Jane Lomax<br />
#Chris Mungall<br />
#Simon Twigger<br />
#Tanya Berardini<br />
*GO Advisors<br />
#<b>Larry Hunter</b><br />
#<b>Lynette Hirschman</b><br />
#<b>Barry Smith</b><br />
#<b>David States</b><br />
#<b>Mike Tyers</b><br />
#<b>Craig Neville-Manning</b> (unable to attend)<br />
#<b>Peter Tarczy-Harnach</b><br />
#<b>Ian Dix</b> (Courtland Yockey attending)<br />
*NIH Representative<br />
#Peter Good<br />
*Other possible attendees<br />
#Monte Westerfield?<br />
<br />
== Venue ==<br />
Accommodation: [http://www.scinns.com/universi.htm Silver Cloud Inns / Seattle-University Village]<br />
<br />
5036 25th Avenue NE<br />
Seattle, WA 98105<br />
Phone: 206-526-5200</div>Simonthttps://wiki.geneontology.org/index.php?title=GO_Advisors_Meeting&diff=5776GO Advisors Meeting2006-08-28T20:21:27Z<p>Simont: /* Aim of the meeting */</p>
<hr />
<div>== Aim of the meeting == <br />
The main focus of this meeting is to obtain our advisors views and perspectives on the work we have planned (i.e. the new proposal) and the approach we are taking to accomplish our aims. <br />
<br />
Please add items below that you think need to be presented. When possible, please put your request in priority rank order:<br />
<br />
'''''Utility for Biologists'''''<br />
<br />
The highest priority for the GOC identified by grant reviewers and others is to enhance the ability of non-informatics biologists to access the GO resources as part of their data analysis efforts. Some of the participants in the GO Consortium provide access to GO data analysis tools as part of their MOD resource. But the GO site itself does not support data analysis directly from the site. We do provide listing of tools, but have not seen it as part of our 'mission' to support a general tool [such as GO TermFinder, for example] as part of the GOC. Should we do so? Wouldn't this be analogous to provide a BLAST server? While the individual MODs have a role to play here, the GOC is seen by some to be behind in supporting the work of the bench biologist.<br />
<br />
* I think this should be given a high priority for discussion. In the AmiGO WG we've discussed adding simple tools (e.g. a cgi of map2slim) to AmiGO, but for some of the more complex tools e.g. microarray tools it's probably not worth developing our own as so many good tools already exist. But should we 'endorse' some of these existing tools? And then how could we have say in the direction they're developed? We already work fairly closely with some of these groups (Onto-Express, GoMiner).<br />
* Related to the list of tools, its great to have this long list but it makes it very hard for new users to know which to use and why. Some sort of critical review of features and suggested uses would be very handy. Selecting/Endorsing a 'best' tool in a given category (if there was/were clear winners) would also be really helpful to users but maybe more controversial if done by GOC vs some external author.<br />
<br />
'''''Utility for GO-Tool Developers'''''<br />
<br />
This is a note from a developer...<br />
"we are in the process of making improvements to our GO analysis tool, the<br />
Ontologizer, and I have noticed that one of the most time consuming<br />
aspects of the process seems to be finding good datasets with which to<br />
test new algorithms. I would guess that we are not entirely alone in this.<br />
I wonder if it would be a good idea for the GO community to make a<br />
repository of datasets for testing new algorithms and also for new users<br />
to learn the ropes. I would be thinking of lists of study sets (say<br />
differentially expressed genes) with corresponding population sets (say<br />
all genes on the chip) together with short biological and methods<br />
descriptions. Does such a repository already exist or does anyone have any<br />
tips?"<br />
<br />
'''''Should GO capture the context of activity'''''<br />
<br />
Is there a facility to construct GO annotations which would capture the context in which a given gene product is associated with (e.g.) a given function? Thus, for example, instead of annotating protein X to oxygen transport [function] one might annotate:<br />
<br />
<protein X in cell component Y> to oxygen transport [function'] <br />
<br />
For MGI, this information is captured for cell types, anatomy and target molecules, but it is not a GO-wide policy. MGI captures this information in structured notes. So, for example MGI curators can make an annotation for gene product X having some function in oxygen transport in a lung epithelial cell. The hope is that if X is also annotated to oxygen transporter activity in lung epithelial cell and plasma membrane of a lung epithelial cell, then we can draw a conclusion that X has the potential to execute a function of an oxygen transporter involved in oxygen transport in the plasma membrane of a lung epithelial cell. In the right spatio-temporal context, the function will be executed.<br />
<br />
<br />
'''''Encouraging community annotation'''''<br />
#How can we help community scientists to get credit for their GO work? Could we publish a short account of the work of individual content meetings with all experts having author credit? Could groups providing manual annotation of their own gene products of interest get a small publication giving an account of their contribution and of possible applications?<br />
<br />
'''''Annotation Tool'''''<br />
#Who is the target audience for the annotation tool?<br />
#How does the idea of an annual functional annotation tool bake-off sound to you? How would you approach it? Can it be used to keep orphaned genomes up-to-date?<br />
#Almost everyone agrees that the GO Consortium should develop an annotation tool, [but not all people since most groups do annotation within the context of their genome annotation stream] Once we begin asking questions about what the tool should do, it becomes clear that every group has very different ideas about what such a tool should do. Groups within the GO tend to advocate for the development of a tool that satisfies their own research efforts at the moment, because that is the immediate need as they understand it. Could the advisors suggest a way of determining which of these special-purpose applications are best for the GO user community ''as a whole'', so that we can decide how to focus our development efforts? What's the best way to encourage inter-group communication to foster collaboration on tools and minimize redundant development efforts? How can we decide whether specific, highly targeted annotation tools or general, lowest-common-denominator annotation tools would be most useful to our user community?<br />
<br />
== Agenda ==<br />
In order to meet our objectives, we need to present all of the material in the morning.<br />
The presentations will focus on the goals and progress of the Consortium and will reflect the new organization and management of the GOC developed through the process of writing the GO Consortium competitive renewal. The times noted here are expected to be divided between a short presentation and then focused discussion on the topic.<br />
<br />
<br />
** - 8:00AM: Introductions (picture on display and circle everyone)<br />
** - 8:10 AM: Overview of Grant Aims (Michael-20 minutes)<br />
** - 8:30 AM: Reference Genomes (Rex - 30 minutes)<br />
** - 9:00 AM: Ontology/Database Developments - Biological (Midori and David-30 minutes)<br />
** - 9:30 AM: Ontology Developments – Technical (Chris-30 minutes)<br />
** -10:00 AM: Break (15 min)<br />
** -10:15 AM: Emerging Genomes (Jen-20 minutes)<br />
** -10:35AM: User Advocacy including AmiGO (Eurie & Jane- 20 minutes)<br />
** -10:55AM: New management structure (Suzi- 20 minutes)<br />
** -11:15AM: Summary of issues we face: pink sheets and more (Judy- 20 minutes)<br />
** -11:35AM: Open Discussion (all)<br />
** -12:30PM – 1:30PM, working lunch for Advisors and GO-top<br />
<br />
** - 1:30PM - 3:00PM, Advisors powwow<br />
** - 3:00 PM - break<br />
** - 3:30PM - 5:00PM, feedback from Advisors<br />
** - 6:00PM dinner with everyone<br />
<br />
== Participants ==<br />
*GO representatives<br />
#Michael Ashburner<br />
#Judy Blake<br />
#Eurie Hong<br />
#Suzi Lewis<br />
#Rex Chisholm<br />
#Jen Clark<br />
#Midori Harris<br />
#David Hill<br />
#Ben Hitz (representing production services)<br />
#Jane Lomax<br />
#Chris Mungall<br />
#Simon Twigger<br />
#Tanya Berardini<br />
*GO Advisors<br />
#<b>Larry Hunter</b><br />
#<b>Lynette Hirschman</b><br />
#<b>Barry Smith</b><br />
#<b>David States</b><br />
#<b>Mike Tyers</b><br />
#<b>Craig Neville-Manning</b> (unable to attend)<br />
#<b>Peter Tarczy-Harnach</b><br />
#<b>Ian Dix</b> (Courtland Yockey attending)<br />
*NIH Representative<br />
#Peter Good<br />
*Other possible attendees<br />
#Monte Westerfield?<br />
<br />
== Venue ==<br />
Accommodation: [http://www.scinns.com/universi.htm Silver Cloud Inns / Seattle-University Village]<br />
<br />
5036 25th Avenue NE<br />
Seattle, WA 98105<br />
Phone: 206-526-5200</div>Simont