EcoliWiki December 2015: Difference between revisions
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Revision as of 16:19, 18 December 2015
Overview: 1. Staff:
Jim Hu Suzi Aleksander Debby Siegele Peter Karp Ingrid Keseler Markus Krummenacker
All of the above contribute to curation; none of the EcoliWiki/EcoCyc staff are funded by GO. 2. Annotation Progress 09/14 mined on 8 September 2014 12/15 mined on 14 December 2015
<protect>
| Annotations | Non-IEA/Non-ND | IEA | ND | All ECs |
|---|---|---|---|---|
|
BP (12/14) |
4791 |
10049 |
0 |
14840 |
|
BP (12/15) |
6548 |
11266 |
0 |
17814 |
|
change |
+1757 |
+1217 |
0 |
+2974 |
|
MF (12/14) |
6827 |
13310 |
1 |
20138 |
|
MF (12/15) |
8163 |
12934 |
1 |
21098 |
|
change |
+1336 |
-376 |
0 |
+960 |
|
CC (12/14) |
1808 |
9190 |
0 |
10998 |
|
CC (12/15) |
4661 |
9377 |
0 |
14038 |
|
change |
+2853 |
+187 |
0 |
+3040 |
|
All Aspects(12/14) |
13426 |
32549 |
1 |
45976 |
|
All Aspects(12/15) |
19372 |
33577 |
1 |
52950 |
|
change |
+5946 |
+1028 |
0 |
+6974 |
| edit table |
</protect>
3. Methods and strategies for annotation
(please note % effort on literature curation vs. computational annotation methods)
a. Literature curation: EcoCyc annotates directly from the literature, currently citing 30,224 individual references for 4500 genes. EcoCyc works to document biochemical pathways in their entirety, and uses a mini-review format in addition to GO to capture as much information as possible. EcoCyc is dedicated to Escherichia coli K-12 MG1655, whereas EcoliWiki incorporates annotations from EcoCyc but also annotates other Escherichia coli strains as well as numerous bacteriophage proteins. Annotations from both sites for taxon 8333 are submitted in the gene_association.ecocyc file.
Effort: 100%
b. Computational annotation strategies: EcoliWiki focuses on manual annotation, so computational annotation is not a priority. The IEAs produced by UniProtKB are assimilated into the GAF and resubmitted.
Effort: 0%
c. Priorities for annotation: EcoliWiki and EcoCyc work to annotate all literature across the entire genome. EcoCyc emphasises annotation of transcriptional regulation, transporters, and metabolic pathways.
4. Presentations and Publications
a. Papers with substantial GO content
b. Presentations including Talks and Tutorials and Teaching
c. Poster presentations
5. Other Highlights:
A. Ontology Development Contributions: EcoliWiki contributes to discussions on the GitHub (previously SourceForge) trackers, as well as bringing attention to potential issues with terms and the ontology as we become aware of them.
B. Annotation Outreach and User Advocacy Efforts: EcoliWiki operates another wiki, GONUTS (Gene Ontology Normal Usage Tracking System), which is available to the general public as a way to access the ontology and existing annotations for all proteins, regardless of organism, currently in UniProt. GONUTS facilitates the addition of annotations and usage notes to terms, journal articles, and proteins. EcoliWiki also promotes annotation through CACAO, a course hosted at Texas A&M University on the GONUTS website. CACAO (Community Assessment of Community Annotation with Ontologies) teaches mainly undergraduate and graduate students, both at Texas A&M and remotely worldwide, not only how to utilise the Gene Ontology but also to improve the Ontology. To date, over 1200 users have edited the GONUTS wiki, and 3848 manual annotations have been submitted to EBI for propagation. CACAO students have had numerous New Term Requests approved and also have identified errors in term definitions and ontology structure.
C. Other Highlights: