Difference between revisions of "EcoliWiki"

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(Mouse Genome Informatics Summary, 2009 draft)
 
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= EcoliWiki Summary, 2009 draft=
+
[[Category:Reports]]
 +
= Staff =
 +
'''EcoliWiki & GONUTS Operation:'''
  
= Overview =
+
James C. Hu
  
= Staff: =
+
Daniel Renfro
 +
 
 +
Nathan Liles
 +
 
 +
Amanda Supak
 +
 
 +
Jieyu Wang
 +
 
 +
Chanchala Roy
 +
 
 +
'''Annotators:'''
 +
 
 +
Debby Siegele
 +
 
 +
Brenley McIntosh
 +
 
 +
Adrienne Zweifel
  
 
= Annotation Progress =
 
= Annotation Progress =
 +
{| border="1" cellspacing="0" cellpadding="5" align="center"
 +
! Year
 +
! Gene Products
 +
! # of GPs with only IEA
 +
! # of GPs with manual annotations (not IEA)
 +
! # GPs with an annotation (IEA or other)
 +
|-
 +
| 2009
 +
| 4482
 +
| 1870
 +
| 1625
 +
| 3495
 +
|-
 +
| 2010
 +
| 6093
 +
| 1755
 +
| 2042
 +
| 3799
 +
|}
 +
 +
=Methods and strategies for annotation=
 +
At EcoliWiki, we have prioritized the RefGenome genes for annotation first.  These genes are listed on our Home Page after they are provided to us by the RefGenome group.  We annotate the most recent genes first and work on previous genes whenever possible.  Other genes not included in the RefGenome list are also annotated.  When a gene product is annotated, we often contact the corresponding author to invite her/him to add/delete/change annotations based on their expertise from working directly with this gene product.
 +
 +
We have also designed an international annotation competition called [http://ecoliwiki.net/colipedia/index.php/Cacao CACAO] (Community Assessment of Community Annotation with Ontologies) that has life science students annotating gene products using GO.
  
 +
= Presentations and Publications =
 +
[[GO_2009_Publications,_Tutorials_%26_Workshops,_Presentations,_Posters,_and_Resources]]
  
==Methods and strategies for annotation==
+
= Ontology Development Contributions=
 +
Debby and Jim have been contributing to ontology development and discussions on electron transport and binding terms.  Brenley has been involved in the virus ontology term development.
  
 +
= Annotation Outreach and User Advocacy Efforts=
 +
EcoliWiki puts a list of the Reference Genome genes in ''E. coli'' on the [http://ecoliwiki.net/colipedia/index.php/Welcome_to_EcoliWiki EcoliWiki Home Page] each month.  EcoliWiki also emails recent authors and requests participation in GO annotation.
  
= Presentations and Publications =
+
CACAO (Community Assessment of Community Annotation with Ontologies) - course designed to have students (undergraduate or graduate) annotate gene products under supervision and review of professional curators.  Pilot course (April 2010) involved undergrads from Texas A&M.  Full course (Fall 2010) involved 16 students from TAMU, 5 grad students from University College London.  Full course (scheduled for Spring 2010) will involved undergrads from TAMU, Nilton Lins (Brazil), Miami, and other undergrad institutions.  DS, JH & BM attended ASM-CUE & ASM GM and offered a booth to encourage use of EcoliWiki and discuss CACAO.  BM presented a poster at the Phage Meeting (Cold Spring Harbor, NY) about CACAO and spoke to several interested faculty.  BM travelled to Brazil in Nov to initiate involvement of undergraduates from Nilton Lins University in the competition.
  
 +
= Other Highlights: =
 +
1.  [http://gowiki.tamu.edu/wiki/index.php/Main_Page GONUTS]
  
= A. Ontology Development Contributions:=
+
The Gene Ontology Normal Usage Tracking System (GONUTS) is a web-based resource for researchers using Gene Ontology (GO) terms and GO.  It has expanded from focusing on documentation of GO terms to also become a valuable online database for organisms without their own MOD (model organism database), such as ''Gallus gallus'' .
  
 +
2.  CACAO (Community Assessment of Community Annotation with Ontologies)
  
= Annotation Outreach and User Advocacy Efforts: =
+
We have developed an undergraduate annotation course using GO terminology and EcoliWiki/GONUTS to help students learn the annotation process and study bioinformatics.  Our pilot competition was run in April 2010 with 16 undergraduates from Texas A&M University.  The students annotated gene products from ''E. coli'' for points and then challenged annotations entered by other teams to steal points.  The students added 153 annotations to EcoliWiki and after review by EcoliWiki professional annotators, we accepted 117 annotations.  This fall, CACAO bloomed into an international competition with the addition of 2 teams of graduate students from University College London competing against 6 teams of undergraduates from Texas A&M.  The students added their annotations to our non-organism specific database, GONUTS (http://gowiki.tamu.edu) since the students were able to choose to annotate any protein in UniProt.  The competition just wrapped up after students entered more than 750 annotations and the annotations are currently under review.  After completion of the review, the annotations will be returned to the GOC in a gaf and be available to the various databases.
  
= Other Highlights: =
+
3.  [http://subtiliswiki.net/wiki/index.php/Main_Page SubtilisWiki]

Latest revision as of 11:38, 23 April 2014

Staff

EcoliWiki & GONUTS Operation:

James C. Hu

Daniel Renfro

Nathan Liles

Amanda Supak

Jieyu Wang

Chanchala Roy

Annotators:

Debby Siegele

Brenley McIntosh

Adrienne Zweifel

Annotation Progress

Year Gene Products # of GPs with only IEA # of GPs with manual annotations (not IEA) # GPs with an annotation (IEA or other)
2009 4482 1870 1625 3495
2010 6093 1755 2042 3799

Methods and strategies for annotation

At EcoliWiki, we have prioritized the RefGenome genes for annotation first. These genes are listed on our Home Page after they are provided to us by the RefGenome group. We annotate the most recent genes first and work on previous genes whenever possible. Other genes not included in the RefGenome list are also annotated. When a gene product is annotated, we often contact the corresponding author to invite her/him to add/delete/change annotations based on their expertise from working directly with this gene product.

We have also designed an international annotation competition called CACAO (Community Assessment of Community Annotation with Ontologies) that has life science students annotating gene products using GO.

Presentations and Publications

GO_2009_Publications,_Tutorials_&_Workshops,_Presentations,_Posters,_and_Resources

Ontology Development Contributions

Debby and Jim have been contributing to ontology development and discussions on electron transport and binding terms. Brenley has been involved in the virus ontology term development.

Annotation Outreach and User Advocacy Efforts

EcoliWiki puts a list of the Reference Genome genes in E. coli on the EcoliWiki Home Page each month. EcoliWiki also emails recent authors and requests participation in GO annotation.

CACAO (Community Assessment of Community Annotation with Ontologies) - course designed to have students (undergraduate or graduate) annotate gene products under supervision and review of professional curators. Pilot course (April 2010) involved undergrads from Texas A&M. Full course (Fall 2010) involved 16 students from TAMU, 5 grad students from University College London. Full course (scheduled for Spring 2010) will involved undergrads from TAMU, Nilton Lins (Brazil), Miami, and other undergrad institutions. DS, JH & BM attended ASM-CUE & ASM GM and offered a booth to encourage use of EcoliWiki and discuss CACAO. BM presented a poster at the Phage Meeting (Cold Spring Harbor, NY) about CACAO and spoke to several interested faculty. BM travelled to Brazil in Nov to initiate involvement of undergraduates from Nilton Lins University in the competition.

Other Highlights:

1. GONUTS

The Gene Ontology Normal Usage Tracking System (GONUTS) is a web-based resource for researchers using Gene Ontology (GO) terms and GO. It has expanded from focusing on documentation of GO terms to also become a valuable online database for organisms without their own MOD (model organism database), such as Gallus gallus .

2. CACAO (Community Assessment of Community Annotation with Ontologies)

We have developed an undergraduate annotation course using GO terminology and EcoliWiki/GONUTS to help students learn the annotation process and study bioinformatics. Our pilot competition was run in April 2010 with 16 undergraduates from Texas A&M University. The students annotated gene products from E. coli for points and then challenged annotations entered by other teams to steal points. The students added 153 annotations to EcoliWiki and after review by EcoliWiki professional annotators, we accepted 117 annotations. This fall, CACAO bloomed into an international competition with the addition of 2 teams of graduate students from University College London competing against 6 teams of undergraduates from Texas A&M. The students added their annotations to our non-organism specific database, GONUTS (http://gowiki.tamu.edu) since the students were able to choose to annotate any protein in UniProt. The competition just wrapped up after students entered more than 750 annotations and the annotations are currently under review. After completion of the review, the annotations will be returned to the GOC in a gaf and be available to the various databases.

3. SubtilisWiki