Annotation Conf. Call 2016-11-22
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Bluejeans URL: https://bluejeans.com/993661940
Agenda
- 2016 Progress Reports
- github go-annotation tracker will house and track action items from GO meetings, e.g. USC 2016
- Annotation Consistency Exercise - Sabrina, Zfin
- Publication : PMID-27545838 (https://www.ncbi.nlm.nih.gov/pubmed/27545838)
- presentation: https://drive.google.com/file/d/0B70QUYaXybRYZXdsSUtHMDVHVHM/view?usp=sharing
- model by Sabrina: http://noctua.berkeleybop.org/editor/graph/gomodel:5824c51a00000007
- model by Kimberly: http://noctua.berkeleybop.org/editor/graph/gomodel:5825564b00000062
Minutes
- On call: Barbara, Chris, David H., Doug, George, Giulia, Helen, Jim, Kimberly, Li, Midori, Moni, Paola, Paul T. Petra, Sabrina, Stacia, Suzi, Tanya
Progress Reports
- Organized by aims in accordance with NIH specs
- Google folder has templates
- Groups need to fill out their progress as they have previously, but in the appropriate Specific Aims
- Tables are still very useful for progress reports, but now they can either be embedded in the Google doc or in a separate spreadsheet
- MOD = institution
- Other work that specifically addresses the aims and crosses institutions, e.g. ontology development, annotation, can go directly into the main report
GO-Annotation Tracker on github
- Action items from USC meeting will be tracked on Gene Ontology's go-annotation repo in github
- We will review these action items in coming meetings
Annotation Consistency Exercise
- Zebrafish paper: Fscn1 is required for the trafficking of TGF-β family type I receptors during endoderm formation.
- Key points:
- Each gene product represented in the model must be associated with a molecular function, even if it is to the root node
- Using inferred relations vs making direct connections, for example when a gene product is part_of process #1 that is causally_upstream_of process #2. By inference, the gene product would then also be causally_upstream_of process #2. The inferred relations will eventually be generated.
- Different approaches to LEGO modeling
- Data from a single paper
- Curators would add annotations just from the experiments performed in a single paper
- If desired, TAS annotations can be used to indicate where information is known but not demonstrated in the paper being annotated
- We could possibly use scripts to fill in TAS annotations with experimental evidence when available or perhaps this is a curation task that is well suited for student projects
- Textpresso queries also help with filling in missing experimental evidence
- Data from multiple papers
- A more comprehensive model of the biology can be built this way
- Can be a good QC exercise
- Curators can choose which approach they would like to use
- Data from a single paper
- Experiments in cell culture vs experiments in a cell line - are these treated differently?
- MGI captures cell line in curation notes, but also can be captured in evidence
- LEGO models may display both molecular-level and organismal-level processes
- Would be nice to have some visual cue that distinguishes these