Difference between revisions of "WormBase-Caltech Weekly Calls"
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== November 2, 2016 == | == November 2, 2016 == | ||
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+ | === Micropublication update === | ||
+ | |||
+ | * First Nemametrix micro in for WS257 | ||
+ | * One lined up for WS258 | ||
+ | * Karen and Daniela in touch with e-publishing platforms ([Highwire], Collaborative knowledge foundation), to set up collaborations for the e-journal |
Revision as of 14:35, 3 November 2016
Contents
Previous Years
2016 Meetings
October 6, 2016
Citace upload
- Tuesday, October 25th, 2016
Automated descriptions
- Ranjana working with Juancarlos to run and update automated descriptions pipeline
Intellectual lineage
- First draft up on WormBase development site
Noctua
- Raymond trying to annotate axioms for anatomy function
- How to connect cell types in different organisms to those in C. elegans anatomy ontology?
- Maybe best way is to connect based on biological function, e.g. regulate osmolarity (kidney, excretory cell)
- Raymond attempting to use Noctua to draw relationships between anatomy terms and function
- There's a distinction between annotating to an instance vs. to a class
- Raymond worked on modeling a statement on excretory cell function from WormAtlas
- Question: how much redundancy might we end up with if we annotate to higher level (cell/anatomy function) and lower level (individual gene product function)? There may be, but all of this information is valuable
Expr_pattern model change
- Daniela proposed a CRISPR-Cas9 tag for the expression pattern class as an experiment type
- Would be inline with "Reporter gene", "In situ", "Antibody", etc.
- Probably want "Genome editing" instead of "CRISPR-Cas9" so as to be more generic
- Would a GFP knock-in via genome editing be distinct from "Reporter gene"?
- Could have a super tag "Genome_editing" and sub-tags "CRISPR-Cas9", "Zinc_fingers", "TALEN"
- Maybe we'll just stick with a "Genome_editing" tag
October 13, 2016
Strain requests
- Ranjana sending strain requests to Mary Ann
- Mary Ann processing published strains requested by Ranjana
GO meeting
- Registration is now setup
- Sarah (Torres) could register all WB CIT participants
- Kimberly is helping organize
AGR Portal Use Case working group update
- Working on first use case, basic text search for genes, GO terms, diseases, and orthology groups
- Data is being collected into a "Portal Data" Google drive: https://drive.google.com/drive/u/1/folders/0B9qQtJIEUDEhRnJKWF9NTTVMVGs
- Some MODs providing more data than requested; That's OK, we just want to keep it simple for the first implementation
- We only want, for the first pass, to retrieve genes, GO terms (no GO-gene annotations), diseases (no disease-gene annotations), and orthology groups
- We likely already have enough data for a first pass implementation; not comprehensive data, but that is fine for now
- Disease data dumped from ACEDB, based on Disease Ontology; not comprehensive for OMIM disease list
- We'll eventually want to pull data directly from OMIM and GO
Extending SPELL virtual machine
- Has a lot of data; may be contributing to SPELL downtime
- Could possibly move to the cloud, but we would need a machine in the cloud
- Can only install SPELL on Ubuntu 8; SGD uses RedHat; we can ask them what they're using, how it's working
- Possibly SGD could run a worm instance on their machine(s)
Transgenome
- Junacarlos finished parsing the transgenome data with Daniela
- Checking parse output numbers with the Transgenome group
- Will the expression data be dumped out in the expression GAF? Yes, should be
- Data from Transgenome are not necessarily peer-reviewed; need to make that clear in display
- Some Expr_pattern objects can be linked to WBPerson, if not a WBPaper
- Data in GAF will point to the 2012 Cell paper as a reference for the Transgenome project
- Raymond suspects issues with it; what if users cannot trace data back to source (by looking up the paper)?
- Would be best to link directly to the respective Transgenome database page when displaying their data
- Notes can be added to release notes that the Transgenome data has been added to the database
Micropublications
- Trial with uploading Nemametrix data; aiming in putting data for the next upload (2-4 micro)
- Added micropublication type in the ?Paper class
- Micropublications will acquire WBPaper IDs
- Previous micropublications were only ?Expr_pattern objects; now will be ?Paper objects
- Ideally micropubs. will be indexed by PubMed and enter the WB pipeline through the normal paper route
- Question: create WBPaper objects as soon as accepted? That is plan for now
- Micropubs. will first be hosted by WormBase, but may move to an independent repository (Micropublication: biology)
- Will we display images/figures from micropubs. only or for all papers? We'll need to wait and see
- Could we accommodate any digital data to associate with the micropub.? E.g. data points, plasmid maps, etc.
- Micropubs. text will be marked up as much as possible; what about making all sentences OWL statements?
- Would this be changing the way that authors write papers? Maybe, but should be independent of core micropublication pipeline
- Each micropublication/data/result could be combined as modules to create a larger, more comprehensive narrative
- There is a notion of a "millipublication" that could be a larger narrative from collected micropublications
- One original idea was that micropublications would capture data that people would not otherwise want to publish
- Data submitted as micropublication will not be able to be submitted as another publication later but will be cited as data point
- Micropubs. will be considered primary research article, not just an abstract (equivalent to meeting abstract)
October 20, 2016
AGR search prototype
- URL: http://search.alliancegenome.org/
- Searching "WNT4", then choosing category "Gene Ontology" provides facets for species
- Question is: how are these species associated to the GO terms?
- Associated genes could have a species prefix or indicator
AGR gene page
- There was resistance to creating AGR gene pages
- Some see it as redundant with what is already available elsewhere
- Although we may want to build a foundation gene page and develop from there
- Maybe MODs could develop their respective gene pages to look more like an AGR standard
- One main reason to create AGR is to have a consolidated, consistent, standard view for data, including genes
- Would be good to assemble a user group (or intended audience) to receive feedback from
- Use Case working group has put together some ideas for a gene comparison page, keyed off of orthology group:
Citace upload
- Next Tuesday, October 25th 10am
Curator call next week
- Topic: curation styles
- Curation by paper, by topic, etc.
- Curation inter-dependencies
- Daniela will present for WormBase
- Send ideas to Daniela for her to cover
- Send older slides with relevant information to Daniela
October 27, 2016
AGR Portal Use Case working group
- Working group had call yesterday with Paul Thomas and Judy Blake
- Decision was made to abandon the idea of displaying "orthology groups"/"homology groups"
- Instead we will display a gene-centric page with comparisons of focus gene data with data from all orthologs and paralogs
- Paul Thomas' group had built a prototype for pulling out orthologs with GO info: http://umodtest.usc.edu/
- This prototype returns closest orthologs of a focus/query gene and then displays a table of all GO annotations for all genes
- We would want to display orthologs for a focus gene as well as paralogs
- This display is very similar to the gene comparison page mockup the use case working group had been envisioning, except now the focus will be a single gene, not a PANTHER subfamily
Disease-Strain curation
- Ranjana working on disease-strain associations for WormBase
- Disease group working on the DAF (disease association file) format
- Ranjana will discuss the strain curation pipeline with Mary Ann and Karen
- Will want a unique ID for each strain, especially for when we merge strain data with other MODs
- One solution is to just prefix the strain name with "WBStrain:" to indicate it came from WormBase
Kimberly visiting CA
- Kimberly will be at CIT next Wednesday
- Noctua developers will be around to discuss integration with Textpresso
- Kimberly can send around schedule for the GO meeting
- Would be good for curators to setup a Noctua account before the Noctua workshop (on Nov 7)
- Kimberly will also be at CIT on Tuesday Nov 8th
Paper editor CGI
- Michael had some issues with the paper editor
- Seems to be working now
November 2, 2016
Micropublication update
- First Nemametrix micro in for WS257
- One lined up for WS258
- Karen and Daniela in touch with e-publishing platforms ([Highwire], Collaborative knowledge foundation), to set up collaborations for the e-journal