Annotation outreach group meeting 16th March 2007: Difference between revisions

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Date- 3/16/07<br>
[[Category:Advocacy and Outreach]]
Present- Rama, JenC, Evelyn, Fiona, Pascale, Michelle<br>
Present- Rama, JenC, Evelyn, Fiona, Pascale, Michelle<br>
<br>
== Fiona McCarthy's Meeting Proposal ==
 
 
Fiona mentioned about the proposal she is submitting to conduct a  conference/symposium on Avian geneome and to get the Avian community  together to get a Avian MOD started. Part of this conference would  educate people about GO, how to do annotations etc, a GO annotation  symposium. Funding rules require that they do it in Mississipi State.  There will also be a discussion about the annotation effort in the  Chicken genome meeting to be held in Barcelona in April.<br>
Fiona mentioned about the proposal she is submitting to conduct a  conference/symposium on Avian geneome and to get the Avian community  together to get a Avian MOD started. Part of this conference would  educate people about GO, how to do annotations etc, a GO annotation  symposium. Funding rules require that they do it in Mississipi State.  There will also be a discussion about the annotation effort in the  Chicken genome meeting to be held in Barcelona in April.<br>
<br>
Rama: What is the format of this meeting? What is the role of GO?<br>
Rama: What is the format of this meeting? What is the role of GO?<br>
Fiona- An outreach presentation by GO would be appropriate.<br>
Fiona- An outreach presentation by GO would be appropriate.<br>
<br>
When we seek input/annotations from the community, what is reasonable?<br>
When we seek input/annotations from the community, what is reasonable?<br>
<br>
Evelyn mentioned that John Young (Institute of Animal Research) is  very proactive and contributes annotations for chicken. He also  contacts Fiona about AgBase related questions.<br>
Evelyn mentioned that John Young (Institute of Animal Research) is  very proactive and contributes annotations for chicken. He also  contacts Fiona about AgBase related questions.<br>
Evelyn mentioned that we should be cautious when we ask the research  community to give us annotations or feedback. Chasing bench  researchers for providing annotations can end up taking lot of our  time. Identifying a paper that has GO annotations and sending it to  the annotators is also contributing to the GO. Some people don't  bother if they have to make the detailed annotations.<br>
Evelyn mentioned that we should be cautious when we ask the research  community to give us annotations or feedback. Chasing bench  researchers for providing annotations can end up taking lot of our  time. Identifying a paper that has GO annotations and sending it to  the annotators is also contributing to the GO. Some people don't  bother if they have to make the detailed annotations.<br>
<br>
 
== Community Annotation via Wiki ==
 
How can we use Wikis to get the community to contribute annotations  or data relevant to GO annotations?<br>
How can we use Wikis to get the community to contribute annotations  or data relevant to GO annotations?<br>
<br>
Wiki- Fiona mentioned that when users see a blank page on the wiki,  they hesitate and don't want to be the first person to contribute.<br>
Wiki- Fiona mentioned that when users see a blank page on the wiki,  they hesitate and don't want to be the first person to contribute.<br>
One way to populate the wiki pages is to use data from GeneRIFs and  IHOP so that users can identify papers from that list.<br>
One way to populate the wiki pages is to use data from GeneRIFs and  IHOP so that users can identify papers from that list.<br>
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Rama and Pascale mentioned that the dictybase and SGD wiki pages are  preloaded with basic information about the gene so that their users  don't see a blank page.<br>
Rama and Pascale mentioned that the dictybase and SGD wiki pages are  preloaded with basic information about the gene so that their users  don't see a blank page.<br>
Action Item- send URLs for those wiki pages to the WG<br>
Action Item- send URLs for those wiki pages to the WG<br>
<br>
 
Evelyn brought up the issue of being able to do batch query that she  sent to the go-help desk. People working on human cardiac proteins  want to batch download all the GO annotations for these proteins.  They are biologists and they don't want to do sql query. She sent  them to Princeton GO slim mapper, but it was too slow.<br>
== Batch Queries ==
 
Evelyn brought up the issue of being able to do batch query that she  sent to the go-help desk. People working on human cardiac proteins  want to batch download all the GO annotations for these proteins.  They are biologists and they don't want to do sql query. <br>She sent  them to Princeton GO slim mapper, but it was too slow.<br>
Suggestion- can the goslim mapper be speeded up?<br>
Suggestion- can the goslim mapper be speeded up?<br>
<br>
She sent the user to biomart but that did not do it either.<br>
She sent the user to biomart but that did not do it either.<br>
<br>
We need documentation on how to do such a query or how to make a  query in Biomart.<br>
We need documentation on how to do such a query or how to make a  query in Biomart.<br>
<br>
Pascale mentioned that they have a good tutorial for Biomart at  dictybase that Eric created.<br>
Pascale mentioned that they have a good tutorial for Biomart at  dictybase that Eric created.<br>
Action item for Pascale- send the URL to the group.<br>
Action item for Pascale- send the URL to the group.<br>
<br>
<br>
<br>
[Jen has brought this to the attention of the User Advocacy group.]
Contacting Journals/funding agencies to request/require authors to  submit data to GO. David Hill is working on getting people to be clearabout the date and format of GO that they used in analysis.<br>
 
<br>
== Journals and GO Annotation ==
 
Contacting Journals/funding agencies to request/require authors to  submit data to GO. David Hill is working on getting people to be clear about the date and format of GO that they used in analysis.<br>
JenC- Flowcharts should be our priority.<br>
JenC- Flowcharts should be our priority.<br>
<br>
 
== Flowcharts ==
Fiona- Who is the audience for these flow charts?<br>
Fiona- Who is the audience for these flow charts?<br>
<br>
Jen- anybody who wants to start making GO annotations.<br>
Jen- any body who wants to start making GO annotations.<br>
Fiona- the first step should be to check if somebody else is  annotating that taxonID. Search GOA to see if they are annotating and  take it from there. This aspect should be in the flow chart.<br>
Fiona- the first step should be to check if somebody else is  annotating that taxonID. Search GOA to see if they are annotating and  take it from there. This aspect should be in the flow chart.<br>
<br>
<br>
<br>

Latest revision as of 17:25, 9 April 2014

Present- Rama, JenC, Evelyn, Fiona, Pascale, Michelle

Fiona McCarthy's Meeting Proposal

Fiona mentioned about the proposal she is submitting to conduct a conference/symposium on Avian geneome and to get the Avian community together to get a Avian MOD started. Part of this conference would educate people about GO, how to do annotations etc, a GO annotation symposium. Funding rules require that they do it in Mississipi State. There will also be a discussion about the annotation effort in the Chicken genome meeting to be held in Barcelona in April.
Rama: What is the format of this meeting? What is the role of GO?
Fiona- An outreach presentation by GO would be appropriate.
When we seek input/annotations from the community, what is reasonable?
Evelyn mentioned that John Young (Institute of Animal Research) is very proactive and contributes annotations for chicken. He also contacts Fiona about AgBase related questions.
Evelyn mentioned that we should be cautious when we ask the research community to give us annotations or feedback. Chasing bench researchers for providing annotations can end up taking lot of our time. Identifying a paper that has GO annotations and sending it to the annotators is also contributing to the GO. Some people don't bother if they have to make the detailed annotations.

Community Annotation via Wiki

How can we use Wikis to get the community to contribute annotations or data relevant to GO annotations?
Wiki- Fiona mentioned that when users see a blank page on the wiki, they hesitate and don't want to be the first person to contribute.
One way to populate the wiki pages is to use data from GeneRIFs and IHOP so that users can identify papers from that list.
Example GeneRIF url for human CD28 -http://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=940
Rama and Pascale mentioned that the dictybase and SGD wiki pages are preloaded with basic information about the gene so that their users don't see a blank page.
Action Item- send URLs for those wiki pages to the WG

Batch Queries

Evelyn brought up the issue of being able to do batch query that she sent to the go-help desk. People working on human cardiac proteins want to batch download all the GO annotations for these proteins. They are biologists and they don't want to do sql query.
She sent them to Princeton GO slim mapper, but it was too slow.
Suggestion- can the goslim mapper be speeded up?
She sent the user to biomart but that did not do it either.
We need documentation on how to do such a query or how to make a query in Biomart.
Pascale mentioned that they have a good tutorial for Biomart at dictybase that Eric created.
Action item for Pascale- send the URL to the group.

[Jen has brought this to the attention of the User Advocacy group.]

Journals and GO Annotation

Contacting Journals/funding agencies to request/require authors to submit data to GO. David Hill is working on getting people to be clear about the date and format of GO that they used in analysis.
JenC- Flowcharts should be our priority.

Flowcharts

Fiona- Who is the audience for these flow charts?
Jen- anybody who wants to start making GO annotations.
Fiona- the first step should be to check if somebody else is annotating that taxonID. Search GOA to see if they are annotating and take it from there. This aspect should be in the flow chart.