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| | [[WormBase-Caltech_Weekly_Calls_March_2018|March]] | | [[WormBase-Caltech_Weekly_Calls_March_2018|March]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_April_2018|April]] |
| − | == April 5, 2018 ==
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| − | | |
| − | === GoToMeeting ===
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| − | * Todd would like access to run GoToMeetings
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| − | * Chris can send access credentials and GoToMeeting calendar details
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| − | | |
| − | === Data Mining Tool comparison ===
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| − | * https://docs.google.com/spreadsheets/d/1vBTDBOKfXn9GcdpF1bXI62VEJ7hwyz2hOyAZcoV1_ng/edit?usp=sharing
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| − | * Chris and Ranjana will work on summarized blog post with link to table
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| − | | |
| − | === Neuro Topic Meeting ===
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| − | * Submitting abstract for meeting, due April 13
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| − | * Wen will submit an abstract
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| − | | |
| − | === Rutgers worm meeting ===
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| − | * We spoke to Andrew Singson; mentioned Rutgers meeting
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| − | * Kimberly will look into joining/speaking
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| − | | |
| − | === Andy Golden disease and phenotype submission ===
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| − | * Andy had sent a sample file of alleles with disease and phenotype data
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| − | * Chris discussed phenotype details with Andy
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| − | * Andy will eventually send bulk data submission
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| − | | |
| − | === Chen Institute furniture meeting ===
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| − | * Today at new building; reviewing office furniture
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| − | * Ranjana and Valerio will go
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| − | | |
| − | === Alliance curation ===
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| − | * Paul needs to present on 5-year Alliance plan
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| − | * Maybe could discuss curation plan
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| − | | |
| − | === Seek/modSeek ===
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| − | * Troyanskaya lab; have we been in touch?
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| − | * They may have new version that can be used
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| − | * Paul S. will see her soon; will ask about it
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| − | | |
| − | === Alliance Entity Summaries ===
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| − | * Have been working on gene summaries
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| − | * Do we want to start working on summaries for other entities, like variations?
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| − | * Ranjana can put together some proposal
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| − | | |
| − | === Alliance Tutorial ===
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| − | * For reverse-site SAB meeting (April 23), need a sample query/tutorial
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| − | * April has worked on a script for a tutorial; maybe we can use
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| − | | |
| − | | |
| − | == April 12, 2018 ==
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| − | | |
| − | === Preliminary AGR Tutorial ===
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| − | * https://docs.google.com/document/d/1iwKs7K87DgbDopIzg9uRlZ9eoxbza2Gd05eaEPjpxn8/edit?usp=sharing
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| − | * Document includes screenshots and text, which is subject to change. Voiceover/basic video should be ready by the end of this week. Additional video editing will be added later, including captions, an intro with footage of scientists, and visual aids (eg. arrows, boxes etc.)
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| − | | |
| − | === Alliance data refresh ===
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| − | * Data refresh for 1.4 release
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| − | * Is this for databases that have more frequent updates, such as daily updates? Does this apply to WB at all? Have to ask Kevin Howe if WB will have a data refresh.
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| − | ** Kevin responded: There is a WB refresh for Alliance 1.4 release based on WS264
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| − | | |
| − | === Phenotype graph bug ===
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| − | * Maybe related to https issues
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| − | * May need to update server to serve https requests
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| − | * GitHub ticket: https://github.com/WormBase/website/issues/6326
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| − | * Juancarlos and Raymond working on
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| − | | |
| − | === Essential gene lists ===
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| − | * Several requests for the essential gene list over the years
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| − | * Difficult to query this out of ACEDB
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| − | * Chris generated a Postgres query to pull out all allele-phenotype annotations with "lethal", "sterile" or descendant phenotypes, including meta data including penetrance, background genotype, etc.
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| − | | |
| − | === Acquiring list of ontology term descendants ===
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| − | * Raymond has URL constructor, for private/internal use; will share internally
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| − | * URL will return all ontological descendants, including all "is_a", "part_of", and "regulates"
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| − | * Phenotypes only have "is_a" relationships anyway, so not an issue
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| − | | |
| − | === Gene set enrichment analysis: duplicate genes ===
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| − | * GitHub ticket: https://github.com/WormBase/website/issues/6300
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| − | * Issue where duplicate genes are not removed from input and are displayed in output
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| − | * We want to make clear to users that the duplicates are not counted multiple times in analysis
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| − | | |
| − | === Gene names existing as secondary names for different genes ===
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| − | * Many genes (120+) have primary names that are also secondary names of other genes
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| − | * Causes confusion in terms of data attribution
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| − | * e.g. mdh-1 and mdh-2: mdh-2 has "mdh-1" as an other name even though these are distinct genes
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| − | * May be good for curators to make sure, for their data type, the correct genes are annotated to the correct data
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| − | * Jae will send around list of problematic gene names
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| − | | |
| − | == April 19, 2018 ==
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| − | | |
| − | === Genotype class ===
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| − | * Need for number of use cases
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| − | * Also good to be compliant with other MODs/Alliance members
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| − | | |
| − | === Biocuration ===
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| − | * Meeting minutes [https://docs.google.com/document/d/1U4prvuSfhWp8D9GWAjIepZL4kE0W206o5YVwkse-pcU/edit?usp=sharing]
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| − | * Attn Wen: GEO data interface
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| − | ** May be of more use to Alliance than WormBase; fewer GEO submissions these days
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| − | ** GEO often omits relevant biological background information
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| − | ** Any GEO data sets that are unpublished? Some, not many (6-7 data sets); some have lagged publications
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| − | * Text mining tools
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| − | ** iTextmine
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| − | *** Highly experimental (PhD project)
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| − | ** Pubtator
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| − | *** Similar to Textpresso
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| − | *** Only index (or allow annotations of) abstracts
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| − | *** Solid project; using state-of-the-art technology and techniques
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| − | * Mike Cherry introduced Alliance
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| − | * Not much with community curation
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| − | * OntoChina: ontologies translated to Chinese
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| − | * Pathway icons (Reactome)
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| − | * Technique to identify the most relevant ontology common ancestor
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| − | ** Accounts for information content of each node
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| − | ** Valerio will send publication to Raymond
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| − | * Automated descriptions
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| − | ** We should talk to GO about which data sources should be used to construct statements
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| − | ** Similarly, work with relevant data/curation groups for the respective data types
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| − | ** GO data coming directly from Alliance; may need to come directly from GO
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| − | | |
| − | === Postgres reading access ===
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| − | * Coko will start generating submission forms as part of the platform build, can we have read access to postgres for them to get WB entities?
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| − | * Juancarlos: Can make dumps specifically for the data objects you need, instead of giving full read access
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| − | ** Can create URL that points to all of the needed data
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| − | * Transgenes don't come from name server; from Postgres
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| − | * Current Postgres architecture is not setup for public access
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| − | ** Could accommodate, but need to look into what that entails
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| − | ** Probably need a server and a sys admin
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| − | ** How would it impact our other work/curation?
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| − | ** Security? Passwords?
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| − | ** How much time would we then need to devote to answering user questions, usability, user interface?
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| − | | |
| − | === AFP ===
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| − | * AFP mock http://textpressocentral.org:5000/overview
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| − | * Update to AFP form to allow authors to confirm/validate predicted entities and data types
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| − | * Steer authors towards data submission forms
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| − | * Form layout tries to mirror gene page
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| − | * Can confirm gene references, add new ones
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| − | * Can report gene corrections and gene-sequence connections
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| − | * Would be good to make clear to users what are the validated/accepted entities when confirming entity recognition
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| − | * May be good to have common interface for each section; maybe one interface for data types and another for entity recognition
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| − | * Need to make clear that the "Next" button marks the section as complete
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| − | * Do we offer text fields for authors to indicate where the data is in the paper? May be asking too much and difficult to implement
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| − | * Do we specify species for data types to verify it is relevant to C. elegans (e.g. physical interactions)? Again, may be asking too much; issue with what the flagging criteria are
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| − | | |
| − | | |
| − | == April 26, 2018 ==
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| − | | |
| − | === Alliance reverse site visit ===
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| − | * Went well, positive response
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| − | * Good feedback on automated gene descriptions
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| − | | |
| − | === Automated gene descriptions ===
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| − | * Where is data coming from? GO data, from Alliance or GO?
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| − | ** Part_of relationships not loaded into Alliance GO data
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| − | ** Federated data vs. centralized data issues
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| − | * Involves architecture discussions and decisions
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| − | * Using same lowest-common-ancestor algorithm as GO
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| − | * Newer WB descriptions are a big improvement
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| − | | |
| − | === WormBase Grant ===
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| − | * There may be a separation of effort/support for tools vs. database
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| − | * Knowledgebase vs. database: which are we?
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| − | | |
| − | === Data Commons ===
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| − | * WB rep? Ask Mike Cherry (cc Kevin)
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| − | | |
| − | === WB SAB ===
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| − | * Lincoln needs head count for SAB
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| − | * http://wiki.wormbase.org/index.php/2018_Advisory_Board_Meeting
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| − | | |
| − | === Noctua 1.0 release ===
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| − | * Noctua 1.0 release coming soon
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| − | * Worm Anatomy ontology; issue with being incorporated into the Uberon ontology
| |
| − | * Worm anatomy terms not available in Noctua table annotator
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| − | * Kimberly will send relevant GitHub ticket to Raymond
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| − | * Raymond will follow up with Chris Mungall
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| − | | |
| − | === Alliance phenotype face-to-face ===
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| − | * June 13-14 in Eugene, Oregon
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| − | * Working group will discuss initial and long term plans
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| − | * Chris & Ranjana plan to go
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| − | * Discuss travel with Sarah Torres
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| − | | |
| − | === Datomic widgets ===
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| − | * Juancarlos discussed person_lineage widget with Adam at length on Monday.
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| − | * Adam says about 90% complete, about 20 to go.
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| − | | |
| − | === WS266 Citace upload ===
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| − | * Deposit files for Wen by May 15th, 10am Pacific time
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| − | | |
| − | === WormBase curator candidate ===
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| − | * Meet with her next Thursday
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