Difference between revisions of "WormBase-Caltech Weekly Calls"
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===AmiGO verification manager=== | ===AmiGO verification manager=== | ||
− | + | The GO verification manager creates a co-annotation matrix that highlights GO annotation intersections. From the matrix, it is easy to see where there are no or many co-annotations. From this analysis, PomBase built rules for future annotation, where if an annotation is made that has already been shown to never have occurred in conjunction with another annotation, an alert is sent. The curator can then reassess the annotation, either fixing it, or adjusting the rules.<br> | |
+ | |||
Poster by PomBase Val Wood on GO annotation rules built through a co-annotation analysis. | Poster by PomBase Val Wood on GO annotation rules built through a co-annotation analysis. | ||
<br>I'm thinking this would be a good tool for analyzing and setting rules for phenotype annotation. | <br>I'm thinking this would be a good tool for analyzing and setting rules for phenotype annotation. | ||
Line 109: | Line 110: | ||
===Reactome training sessions=== | ===Reactome training sessions=== | ||
Peter D'Eustacio is setting up WebEx training sessions for curating in Reactome for the different MODs- this includes WB, SGD, Flybase and PomBase, at least. Right now the thought is that there will be a couple intro WebEx sessions, and eventually an in-person curate-athon (jamboree) where all curators will get together and do a shared project (place to be determined). I will definitely be participating, but this can be open to anyone. | Peter D'Eustacio is setting up WebEx training sessions for curating in Reactome for the different MODs- this includes WB, SGD, Flybase and PomBase, at least. Right now the thought is that there will be a couple intro WebEx sessions, and eventually an in-person curate-athon (jamboree) where all curators will get together and do a shared project (place to be determined). I will definitely be participating, but this can be open to anyone. | ||
+ | |||
+ | ===Fission Yeast Phenotype Ontology (FYPO)/PATO=== | ||
+ | Should we move to PATO? | ||
+ | The FYPO has recently been [http://bioinformatics.oxfordjournals.org/content/early/2013/06/03/bioinformatics.btt266.full#T1 published]<br> | ||
+ | You can download the ontology on the OBOfoundry [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fypo here]<br> | ||
+ | (to open it in oboedit, you need to set an advance setting to allow danglers)<br> | ||
+ | At first it seems pretty chaotic, but after a bit I found it makes a lot of sense- the branches are all different views and access points to the phenotypes. The phenotypes themselves are composed of different ontologies, GO, ChEBI, CL (Cell) and PATO qualities, so terms from these ontologies are used as 'parent' terms. There is also, of course, the phenotype branch itself along with a quality branch. I think this organization actually makes the ontology more accessible to people as it lends itself to being approached from different vantage points. | ||
+ | |||
+ | I think it would be good for us to invest in moving our phenotype ontology to be PATO compliant, and I think FYPO offers an excellent example for organizing it. |
Revision as of 19:07, 16 April 2014
Previous Years
2014 Meetings
April 3, 2014
WOBr
- Testing at juancarlos.wormbase.org (from there go to Tools > Ontology Browser)
- As one-offs, Raymond can take newly generated GAFs from curators and process for testing.
Murray Expression datasets
- Still need to acquire primary expression data from Waterston lab
- Problems with handling inferred expression of genes in cells
- Thus inferred expression data will be removed
- Expression object will retain graphical representations supplied by Murray et al.
- A friendly reminder will be sent to Waterston requesting tabulated, processed primary expression data.
April 10, 2014
Apologies
- Karen: attending impromptu OICR group meeting, won't be on the Caltech call.
BioCurator Meeting
- many text mining tools
- many ontology systems, mapping ontologies
- Aging ontologies
- Anatomy ontology mapping (Uberon)
- Format convergence? OBO, OWL, RDF? Plugin for Protege to read OBO files
- How extensive is OWL? How much has OWL been applied to biology? OWL is being used for reasoning
- Community Annotation
- CANTO (Community ANotation TOol) workshop (Wen attended)
- PombeBase use CANTO and works well
- CANTO (Community ANotation TOol) workshop (Wen attended)
- Big data curation open discussion/workshop
- Enormous datasets (e.g. genome sequencing of all cancer patients)
- Data storage issue
- Data stability issue
- Clinical data, portal set up by Michael Cherry, ClinGen
- Lincoln's talk
- International Cancer Genome Consortium (ICGC) project (petabyte datasets)
- 10,000 cancer patients already sequenced (18 PB by 2018)
- Torent P2P data sharing
- BioCreative workshop
- Text mining
- Pubtator (http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/index.cgi?user=User425569566)
- Curates sentences, marks up entities, only applied to abstract
- Pubtator (http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/index.cgi?user=User425569566)
- GO annotation
- GO Cat (http://eagl.unige.ch/GOCat/)
- Text mining
- Amazon "Mechanical Turk" community annotation
- EcoCyc, MetaCyc - pathway curation (will hear from Karen)
- Reactome
- May be a good tool for displaying TF-target gene interaction display (vs. Cytoscape)
- Add a Reactome display to WormBase?
- SPELL - anything to replace SPELL? No.
- Still lacking other tools for microarray and RNA-Seq data
Heartbleed SSL security issue
- Raymond updated all servers/machines
- All machines need to be rebooted
- Any user passwords should be changed
- Do we care about any non-root users? Best to change all passwords on machines that have been updated
BioGrid C. elegans physical interactions
- Kimberly has been using BioGrid's curation tool
- We have a table of C.elegans large scale genetic and physical interaction data
- We're still trying to get all data
Timestamps
- Curator evidence vs. history of curation
- Kevin and Juancarlos still looking for use-cases
- Need to consider for future database migration and potential use of a common central database
- Curators use timestamps for culling out bogus data objects/cleaning up data
April 17, 2014
Agenda
- BioGrid
- AmiGO
- Reactome
- BioCurator Meeting
BioGrid followup
What are the roadblocks to protein-protein interaction curation and incorporation into WormBase?
AmiGO verification manager
The GO verification manager creates a co-annotation matrix that highlights GO annotation intersections. From the matrix, it is easy to see where there are no or many co-annotations. From this analysis, PomBase built rules for future annotation, where if an annotation is made that has already been shown to never have occurred in conjunction with another annotation, an alert is sent. The curator can then reassess the annotation, either fixing it, or adjusting the rules.
Poster by PomBase Val Wood on GO annotation rules built through a co-annotation analysis.
I'm thinking this would be a good tool for analyzing and setting rules for phenotype annotation.
http://amigo2.berkeleybop.org/cgi-bin/amigo2/matrix https://sourceforge.net/apps/trac/pombase/wiki/MatrixProject http://build.berkeleybop.org/job/check-shared-annotations/lastBuild/console
They can include worm checks in this project as well. I don't know what we would need to do for that.
I can send along Val's poster to anyone who wants to know more
Reactome training sessions
Peter D'Eustacio is setting up WebEx training sessions for curating in Reactome for the different MODs- this includes WB, SGD, Flybase and PomBase, at least. Right now the thought is that there will be a couple intro WebEx sessions, and eventually an in-person curate-athon (jamboree) where all curators will get together and do a shared project (place to be determined). I will definitely be participating, but this can be open to anyone.
Fission Yeast Phenotype Ontology (FYPO)/PATO
Should we move to PATO?
The FYPO has recently been published
You can download the ontology on the OBOfoundry here
(to open it in oboedit, you need to set an advance setting to allow danglers)
At first it seems pretty chaotic, but after a bit I found it makes a lot of sense- the branches are all different views and access points to the phenotypes. The phenotypes themselves are composed of different ontologies, GO, ChEBI, CL (Cell) and PATO qualities, so terms from these ontologies are used as 'parent' terms. There is also, of course, the phenotype branch itself along with a quality branch. I think this organization actually makes the ontology more accessible to people as it lends itself to being approached from different vantage points.
I think it would be good for us to invest in moving our phenotype ontology to be PATO compliant, and I think FYPO offers an excellent example for organizing it.