WormBase-Caltech Weekly Calls
From WormBaseWiki
Contents
- 1 Previous Years
- 2 2015 Meetings
- 2.1 September 3, 2015
- 2.1.1 Development instances at Caltech
- 2.1.2 GObA (Graph of Ontology-based Annotations)
- 2.1.3 Anatomy enrichment tool
- 2.1.4 Community allele-phenotype annotations
- 2.1.5 Logical Extensions of Gene Ontology (LEGO)
- 2.1.6 Phentoype-association file: Attributing phenotypes to genes via genetic interaction
- 2.2 September 10, 2015
- 2.3 September 17, 2015
- 2.4 September 24, 2015
- 2.1 September 3, 2015
Previous Years
2015 Meetings
September 3, 2015
Development instances at Caltech
- Caltech wants to provide a Beta testing environment for curators/users. we'll have to rely on juancarlos.wormbase.org as cost/benefit analysis is unfavourable to consider other options.
GObA (Graph of Ontology-based Annotations)
- Added a couple new graph types
- Working out details before sending out to Beta testers
- Example pages:
Anatomy enrichment tool
- Enter list of genes, get a list of anatomy terms
- Developed originally by David Angeles
- Being incorporated and worked on by Raymond
Community allele-phenotype annotations
- Outreach: sending out e-mails to relevant people
- Not done yet
- May be good to travel out to labs to give instructions, outreach
- We'll gather a list of labs that publish phenotypes and contact them
- We can also push the micropublication process
Logical Extensions of Gene Ontology (LEGO)
- Further developments being made on Noctua and other LEGO software
- Lots of discussion on LEGO modeling, how to best do it
- Testing is scheduled
- Protein complexes in cellular component ontology?
- GO will collaborate with Protein Ontology group to work out how to capture that info
- Molecular function ontology annotation approach is being refactored
- Noctua being used for phenotype annotations, would be good to see how
Phentoype-association file: Attributing phenotypes to genes via genetic interaction
- Can we (and how do we) capture genes as involved in a process, for example, SynMuv genes in vulva development
- The phenotype association file currently only on direct phenotype annotations, not interaction-based phenotypes
- Gene Ontology captures these events (associations to a process, for example) with the evidence code, Inferred from Genetic Interaction
September 10, 2015
E-mail "blitz" for community forms
- Ranjana & Kimberly are composing e-mail to PIs for concise description
- Chris is going to e-mail first authors for allele-phenotype contributions
SObA (Summary of Ontology-based Annotations)
- E.g. daf-2: http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000898
- Daniela asking for a zoom option to see names of smaller nodes in "weighted" graph
- We cannot do this currently
- It may be possible to develop this; will need to test
Anatomy/Tissue enrichment tool
- Counting genes annotated to a term, selecting terms with 100+ annotations
- Reason parent-child, ancestor-descendant relationships; keep most granular terms (remove ancestors)
- Create table of genes (~4,000) annotated to these terms (genes in rows, anatomy terms in columns)
- Take ?Expression_clusers/studies based on anatomy terms, take genes from that set as a test query (positive control)
- Using HSN neuron expression set, were able to retrieve HSNL and HSNR, as well as another terms
- Need to be aware of ?Expression_clusters that represent depletion rather than enrichment
EQ-PATO-style annotations
- Phenotype and RNAi OA's have been updated on the sandbox
- Data models have been proposed
- Awaiting model approval to move ahead
Yeast-One Hybrid data from Walhout lab
- We will be getting data from Marian Walhout in the next couple of weeks
- We hope to be up-to-date on all the Y1H data from her lab soon
WormBook chapter reviews
- Some reviews have come in
- Most we are still waiting on
modSeek & SPELL
- Klaus Richter has been using SPELL to annotate a list of 200-300 genes
- SPELL was periodically frozen; problems from Yahoo web-indexing
- Klaus wanted a standard file listing the most correlated genes for each gene in WormBase
- Cannot use SPELL for this, but we can use Seek
- Would be great to see expression correlation incorporated into the Cytoscape network viewer
- Will try to establish a pair-wise correlation table of all protein-coding genes (~20,000x~20,000)
- Maybe web can read off of such file
September 17, 2015
WormBook changes [Paul S]
- What could we do with the new changes?
- Worm Breeder's Gazette?
- Jane & Todd working on streamlining process of submission
- GSA wants to publish higher impact chapters
- Egg shell chapter is too detailed (won't generate enough citations for GSA)
- GSA will do a methods chapter on CRISPR (hot topic)
- Go-ahead with incorporation of micropublications?
- We need a name to call it; branding
- Incorporation of pathway/process pages
- Marie-Anne Felix et al. asked for species descriptions
- Mark Blaxter et al. asked for genome announcements
- How will citations work/look?
- Will chapter updates still be possible under GSA? That will be up to GSA
Author first pass incorporation of community curation requests
- We already have a developed Author-First Pass (AFP) pipeline to request data from authors
- We could co-opt the AFP pipeline to request community curation, specifically concise descriptions and allele-phenotype
- We can remake the AFP e-mail to shift focus to concise descriptions and allele-phenotype forms
September 24, 2015
E-mails soliciting contributions
- Can we automate the e-mails for concise descriptions?
- May be better to e-mail manually
- We want to e-mail a smaller group of people before ramping up to mass e-mails
BioCurator meeting
- Geneva, Switzerland
- Mary Ann proposed community curation workshop
- Mary Ann in communication with Pascal
WormBase ParaSite
- Had SAB meeting
- Want to have more integration at the search level
- Want to have a plan for data mining
Datomic
- Thomas had good results with a table maker for Datomic
- We will need a certificate (web security, SSL) to query Datomic at Hinxton
- Thomas wrote an ACEDB-to-Datomic converter; Juancarlos testing with a subset of data
- Accessibility of Datomic information online? Some tutorials and videos available
SObA (Summary of Ontology-based Annotations)
- Raymond acquired expression clusters from Wen to test the (David's) anatomy enrichment tool
- Many expected results, some not
- Considering a SObA-view of genes in a particular expression cluster, using existing annotations
