WormBase-Caltech Weekly Calls
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- 1 Previous Years
- 2 2018 Meetings
- 2.1 May 3, 2018
- 2.2 May 10, 2018
- 2.3 May 17, 2018
- 2.4 May 24th, 2018
- 2.5 May 31th, 2018
GoToMeeting link: https://www.gotomeet.me/wormbase1
May 3, 2018
- Wen was working on simplification of SimpleMine output
- Considering removing general terms in an ontology when more specific terms exist
- Concern that we would be removing information; will keep terms
- Topics in SPELL need some organization, possibly trimming
- We could create a graph (SObA) display of topics (based on GO process)
SPELL problem with WS265
- Wen had to debug; SPELL has limit of how many genes can be processed per data set (46,340)
- Wen trying to accommodate, deleting some genes from data set that had no expression (kludge)
- Wen will write to Matt Hibbs to ask how to deal with
- Will Alliance work together on a system to analyze large scale expression data?
- Will arrive at 10am
- Skype calls with remote curators
- Curators will send group Skype handle and requested time to talk
May 10, 2018
ECO terms for genome editing
- Asking group's feedback on ECO terms for genome editing (Daniela)
- What would be used for fly-enhancer trap experiment?
- Genomically encoded GFP, for example
- ECO: GFP localization
- ECO term, example: Fluorescent protein transcript localization evidence
- Single copy transgene? Endogenous locus?
- Whether it is CRISPR or not may not be relevant
- May request ECO terms that capture distinct types of transgenes evidence
- Will use generic term for now
- Do other MODs use ECO?
- May want to capture endogenous/non-endogenous, multi-copy/single-copy distinctions
- Many of these features are captured in the transgene and construct objects already; specific ECO code redundant?
- Significant involvement in Alliance
- Interest in micropublications; will push a pilot
- June 19, moving from older DB to Postgres
- Investigating automation for some curation processes
- Students review which papers to include; acquire PDF
- Curate paper-by-paper
- Supplement request for year 3, due soon (May 15)
- Formal report from NHGRI, 18-month plan looks good
- Further future plans (from NHGRI perspective) aren't quite clear
- Software infrastructure?
- Central- vs. MOD-control of resources questions
- Likely will have to write a NIH proposal in Fall or Winter
- How much is Alliance going to handle human variants?
- NHGRI interested in metabolomics; Alliance plans?
- Had help desk question about phenotypic screens in organisms other than worms, flies, yeast, bacteria
- There have been human cell line phenotypic screens (e.g. siRNA/shRNA); who curates these, if anyone?
- Also, induced pluripotent stem cell experiments
- Issue came up about assigning unique WBStrain IDs
- Can use a nightly nameserver dump from Hinxton to populate Postgres/OA
- Will need to clean up existing strains in Postgres
- Also, considering unique IDs for genotypes
- Mechanics of naming and managing naming of objects
- Nightly syncing (cronjob) to nameserver
- Ideally, we would have instant updates; Hinxton firewall prevents direct access; Matt working on establishing a separate nameserver location to gain direct access
- Strain names (at least historically) have been updated quarterly from CGC file
- Curators need mechanism to create and use strain (and variation) names right away
- Current system requires manual denormalization step; has worked so far
May 17, 2018
- Create a strain OA? Central curation tool for strain data?
- Would need to maintain synchrony with CGC and Hinxton
- Postgres/Tazendra variation adding CGI: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
- Will add similar link for Strains, adding info to obo_name_strain and obo_data_strain as well as a tempfile, which will those objects in postgres when the nightly_geneace.pl updates the OA strain info
- Who will present? Present what?
- We can generate a central document with stats to give to SAB
- Ask SAB for opinions and guidance?
- Would be good to assess current efforts and priorities, ask if we should stay the course or make modifications to our approach
May 24th, 2018
- Not sure if this falls under content....
- User asked about phenotype information being incorporated into the gene description
- Chris directed him to phenotype submission form; he has since submitted the phenotypes
- Phenotype data hasn't yet been incorporated into the automated descriptions pipeline
- We can direct him to the gene description submission form
- Ranjana will respond to user email
- Will likely swap out older WB automated description pipeline with newer Alliance automated description pipeline
- Working on new model for importing RO terms into WormBase
- Question: Do we need to import all of RO?
- For example, RO also has terms from other ontologies:
[Term] id: GO:0003674 name: molecular_function is_a: BFO:0000015 ! process property_value: IAO:0000589 "molecular process" xsd:string
- Question: How much term information do we want and/or need?
- For example:
[Typedef] id: BFO:0000050 name: part of def: "a core relation that holds between a part and its whole"  property_value: IAO:0000111 "is part of" xsd:string property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: IAO:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string is_transitive: true is_a: RO:0002131 ! overlaps inverse_of: BFO:0000051 ! has part
- For curation, we could import only the BFO and RO ID spaces of RO, but include all of the tag-value pairs (the usage examples might be helpful)
- For WB, though, we could injest only the BFO and RO ID spaces of RO, and only include in the model: id, name, def, is_a, domain, range, and inverse_of tags
- We can always link out from WB to pages with more detail on RO terms
- Will use RO ids in ?GO_annotation model in the Annotation_relation part (model will need an update)
- The ?GO_annotation model also refers to relations used in annotation extensions. Unfortunately, though, not all annotation extension relations are in RO, so we can't yet use RO in this part of the model.
- We can either import these other GO relations as a separate class, or import them if/when they get included in RO (there is a PRO/RO meeting scheduled for late October with some preliminary phone conferences prior).
- The Alliance Gene Expression group is also dealing with this issue.
- Where can we use RO terms in other curation models?
- Kimberly will add to the agenda for the next WB site-wide conference call
Methods in Molecular Biology book
- Eukaryotic Genome Databases, has WormBase chapter
- Book arrived at Caltech
- Chris will ask publishers about getting PDFs without watermarks
ICBO 2018 meeting
- International Conference on Biological Ontology (2018)
- Raymond considering submitting abstract
- Not clear if it needs to be a full paper; can we resubmit Biocuration meeting abstract?
- Can the content be published elsewhere once submitted to the meeting?
May 31th, 2018
Feedbacks from Front Range Worm Meeting
- Is it possible to collect old theses online and load them into Textpresso?
- Shall we suggest authors put "elegans" in titles and abstracts? Min Han said some of his papers do not have this keyword.
- Community curation. Erin Osborne Nishimura mentioned camps and courses for undergraduate research. Can they do allele and phenotype curation for WormBase? Who will follow up with her?
- Shall we send the AFP form to some users for feedback?
Updates about SPELL
- SPELL has a limit of 46340 genes per dataset. Wen had to kluge by removing worm RNAseq gene entries that showed zero in all experiments in a dataset. Microarray and Proteomics datasets do not exceed this limit so they are fine. SGD does not have this problem since yeast only has ~6,000 genes and yeast SPELL only has microarray.
- Wen wrote to Matt Hibbs but he did not respond to the email.
- Mike Cherry said it was not worth to continue to develop SPELL since it is so old. Thus, we will have to continue to kludge until there is a better tool to replace SPELL.
- Mike Cherry proposed to adapt GTEx for AGR. Wen and Edith Wong from SGD are working on a proposal for GTEx to add functions that SPELL already has, and additional functions that we want to have.