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| | [[WormBase-Caltech_Weekly_Calls_August_2018|August]] | | [[WormBase-Caltech_Weekly_Calls_August_2018|August]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_September_2018|September]] |
| − | == September 6, 2018 ==
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| − | === Genotype class ===
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| − | * Chris started initial document to draw up ?Genotype class and make appropriate changes to ?Strain class
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| − | ** https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing
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| − | * Would be good for people to look at so we can discuss next time
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| − | * Would also be good to have Kevin H take a look and provide feedback
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| − | | |
| − | === Citace Upload ===
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| − | * Send citace files to Wen by Sept 18, 10am Pacific
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| − | | |
| − | === Automated gene descriptions ===
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| − | * Group making improvements
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| − | * Added disease, protein domains
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| − | ** When direct experimental evidence for disease relevance, will say "gene has been used to study"
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| − | * When minimal data (information-poor genes), we can refer to human ortholog and data stored for that human gene in Alliance
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| − | * Continue to receive feedback from users; include enrichment information, etc.
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| − | * Now have good trimming algorithms to retain important info without flooding a description with too many granular terms
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| − | * Will not store automated descriptions in Postgres
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| − | * Wen will modify SimpleMine scripts to accommodate change
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| − | * Would be good to write a paper on automated concise descriptions
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| − | * Came up at GO meeting/hackathon: Translating GO-CAM models into concise descriptions?
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| − | ** Should be doable; just need to develop code when we're ready to do that
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| − | | |
| − | === Textpresso presentation at next Alliance all-hands call ===
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| − | * Who should present? Maybe have several people? Kimberly, Valerio, Michael for sections?
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| − | * We can discuss at next Textpresso meeting
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| − | * Should cover techniques and software, but keep it generally simple and comprehensible for a larger audience
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| − | | |
| − | == September 13, 2018 ==
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| − | === Citace upload ===
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| − | * Send files to Wen by 10am Tuesday (18th)
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| − | | |
| − | === Genotype class ===
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| − | * [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?usp=sharing ?Genotype class proposal]
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| − | * Genotype_name tag: free text summary of the genotype
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| − | ** Can this be automatically generated from components? Ideally, yes, but may be difficult
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| − | ** Otherwise, can be manually written, as we have been doing, but is a bit denormalized and may require maintenance
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| − | * Genotype_description tag: free-text description of the genotype
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| − | ** No precedent and probably not going to start now, so will remove from model
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| − | * Genotype_components supertag: to collect genotype component objects and, where necessary, free text
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| − | ** We want to be able to express zygosity for each referenced object, likely requires a #Zygosity hash (and hence a ?Zygosity model)
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| − | ** ?Zygosity model can have three main tags: "Homozygous", "Heterozygous_with_wild_type", or "Heteroallelic_combination_with"
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| − | *** Heteroallelic_combination_with tag could further specify the type and identity of the object that is in heteroallelic combination with the original object
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| − | *** Since it is not ideal to store an arbitrary component in the #Zygosity hash, we should probably just state the zygosity as "Heteroallelic_combination" and for display purposes have an automated way to calculate which components affect the same locus/loci (if necessary)
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| − | | |
| − | == September 20, 2018 ==
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| − | | |
| − | === Kimberly's talk at Rutgers ===
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| − | * Kimberly went to worm meeting at Rutgers (10 labs using C. elegans? 6-7 totally worm-centric)
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| − | * 30-40 attendees (PIs, postdocs, grad students)
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| − | * Discussed tools and features at WB
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| − | * Presented Alliance pages and Textpresso
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| − | * PIs are enthusiastic about WB
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| − | * Monica Driscoll made a good plug for Textpresso
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| − | * People requesting FAQs and user guides (text and videos)
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| − | * Monica suggested a WB tutorial for PIs ;p
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| − | * Some people surprised about what they can accomplish using the tools available, like SimpleMine
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| − | * Covered gene set enrichment, WormMine, SPELL, SimpleMine, ParaSite BioMart, Textpresso
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| − | * Would be good to show people how to use Textpresso Central
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| − | * Discussed micropublications, asked about negative results (precedent?)
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| − | * Some asked about WB funding and Alliance plans
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| − | * Can we make a within-page search available to find, for example, field names etc.
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| − | * Some challenges in find genes/proteins of certain class
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| − | ** Had question about histone genes recently
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| − | ** Repeatedly have had questions about finding "ion channels"
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| − | ** Searching gene class with text pulls out lots of false positives
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| − | ** Could perform an analysis on particular classes of genes (e.g. histones or ion channels) and generate a micropublication providing the curated list
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| − | ** Can generate a WormMine template query to pull these out for each release
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| − | ** What classes of genes would we want to identify: histones, transcription factors, ion channels, protein kinases
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| − | ** Chris will look into WormMine templates using gene class info and look into pulling in protein motif information
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| − | ** We will ask other MODs and UniProt about how they deal with this issue
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| − | | |
| − | | |
| − | == September 27, 2018 ==
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| − | === Update on the new AFP form and pipeline ===
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| − | *Daniela, KImberly, Juancarlos, and Valerio will update on the current status of the new AFP form and pipeline
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| − | **Overall, the goal has been to incorporate as much Textpresso-based entity and data-type flagging as possible into the form
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| − | **Move from author data flagging to author data validation wherever we can
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| − | **Provide opportunities for authors to submit more detailed curation if they want
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| − | * General: Positive thru SVM gets checked checkbox
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| − | * General: Question mark icons with help text
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| − | * Gene recognition
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| − | ** Need to set a threshold of mentions; don't necessarily want all genes mentioned once
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| − | *** Can we show all genes, ranked by occurrence?
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| − | ** Don't want to overwhelm users
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| − | ** How are the genes identified? Via the Textpresso pipeline, string matching, consolidate multiple instances (protein, gene, etc.) into single gene result
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| − | ** Searches include supplemental materials
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| − | ** Cannot search by section of paper
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| − | ** Can we identify genes other than C. elegans/worm? Are not doing now, and will stick to C. elegans for now
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| − | ** Will expand to non-elegans nematodes in future; will expand to other species when extending to other MODs/Alliance members
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| − | ** Chris: should we show the name of the gene as mentioned, verbatim, from the paper?
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| − | *** Karen: No, we should insist authors use the proper names
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| − | *** Chris: Meant referencing sequence names in paper, but public name comes out by the time AFP goes to authors, causing confusion
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| − | ** Can we pull genes from tables? We are pulling from PDF tables, but not supplemental Excel tables, for example
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| − | * Gene model updates: checkbox yes/no
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| − | * Species in paper
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| − | ** Including worm, mouse, human, yeast
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| − | ** Still more work to do on this front
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| − | * Alleles recognized
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| − | ** Show list of allele names and WBVar IDs for confirmation
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| − | ** Can submit new alleles within the AFP form (just allele names, no genes or other info; keeping it simple)
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| − | * Allele sequence change checkbox yes/no (link to Allele sequence info form)
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| − | * Can there be a feedback option readily available? There is a comments section toward the end of the form under "Anything else?"
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| − | * Transgenes handled like alleles
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| − | * Antibodies
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| − | ** Newly generated antibodies checkbox and text field (ask for details? consistency with alleles?) maybe shouldn't ask for antibody details; can make details optional
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| − | ** Form for existing antibodies
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| − | * Expression data
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| − | ** Anatomic expression in WT
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| − | ** Site of action (may be difficult to interpret user input; ask for example; make text details required)
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| − | ** Time of action
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| − | ** RNAseq data
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| − | * Microarrays - just link out to GEO
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| − | * Interactions (all SVM based, three checkboxes)
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| − | * Phenotypes (SVMs, link to phenotype form)
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| − | * Disease
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| − | ** Checkbox for worm orthologs of human disease gene, etc.
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| − | * Comments section (to point out missing data types, provide general comments on form)
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| − | ** Ask for unpublished data and suggest micropublication
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| − | * Final thank you and update contact info and lineage
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| − | * CIT feedback
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| − | ** Maybe make font size larger
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| − | ** Mobile device compatible? Yes
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| − | ** Change "Anything else?" to "Anything else? Comments?"
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| − | ** Can people save and return later? Yes
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| − | *** How do we know they're finished? There is a "Finish and submit" button at end (but authors can still go back and make changes later)
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| − | *** Maybe move "Finish and submit" button to left panel so it is always visible? Maybe make the button stand alone?
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| − | ** If authors indicate there are physical interactions, can we distinguish elegans-elegans interactions vs. non-elegans or interspecies interactions? No, we cannot yet distinguish
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| − | | |
| − | === Genetics and G3 papers in Textpresso ===
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| − | * These papers don't get a PMID yet (when they first enter WB), only DOI (most of time DOI doesn't work (yet))
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| − | * DOI should work right away; Karen will look into if there's a problem/typo
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| − | * Daniel needs to keep track, go back and merge WBPapers once PMID goes live
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| − | * Kimberly or Karen may have to send papers directly to Daniel for uploading
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| − | * Should Daniel only download papers with a PubMed ID? Yes, except for micropublications?
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| − | * Need a separate pipeline for micropublications? Daniel is currently downloading the papers
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| − | | |
| − | === ParaSite (non-elegans) papers ===
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| − | * Should Daniel be trying to download all of these papers? Many are hard to track down
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| − | * Daniel should ask Michael Paulini
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