WormBase-Caltech Weekly Calls June 2016

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June 2, 2016


  • Wen will create ticket to create wormbase.org URL
  • Will go under Tools menu
  • Ranjana will make blog post once it is live

Postgres Timestamps

  • Wen, Chris, and Juancarlos have been working on updating older timestamps for OA entries in Postgres
  • For OA entries generated upon creation of some OA's, the Postgres timestamp is the data of OA creation, not the original data of the object
  • Chris identified all objects from various OAs that had the same initial import timestamp, Wen determined the original ACEDB timestamps for those objects, and Juancarlos is updating the OA entries (curator timestamps) to reflect the object's original timestamp
  • This will be good for consistency going forward and for tracking history of object generation over time

Transgenome project

  • Daniela spoke to developer on project
  • They're fixing/cleaning up data on their end
  • Working on mapping fosmids to latest release of WormBase
  • Probably will import data in a month

UMOD phenotype call yesterday

  • Discussed phenotype data associations
  • Many MODs curate phenotypes to genotype; cannot always make direct, unambiguous associations to a single gene
  • SGD curate to gene, using controlled vocabulary
  • Monarch phenotype data exchange format; can include many levels of detail
  • Common challenge: identifying the single causative agent/mutation

June 9, 2016


  • Wen will make it work off current (live) release of WormBase
  • Do we want to make it more versatile? Add features to specify information to retrieve (specify columns)?
  • Maybe later, but is sufficient for now
  • WormBase official [URL| <http://www.wormbase.org/tools/mine/simplemine.cgi>]
  • Is there a gene # limit? Will test
  • Wen wants to add WormPep ID column; needs to retrieve all WormPep IDs for a gene

Flagging papers for species

  • Going forward, Kimberly, Jane, and Michael will manually flag papers for species
  • Retroactively, papers will be flagged by scripts
  • ~1000 papers not flagged as C. elegans, but likely mentioned in body of paper; Kimberly reviewing
  • These papers often don't have curatable data

Associating genotypes to phenotypes

  • There is increasing need to annotate phenotypes to complex genotypes (not just single alleles/genes, etc.)
  • MGI captures genotype-to-phenotype connections, but can't always attribute a single causative gene
  • We can capture complex genotype phenotypes in interaction objects, but it may be vague to end users
  • Chris will draw up use cases and generate a data model proposal to accommodate

Topic for next curator call

  • Still being voted on via Slack poll
  • Should Doug and Karen decide topic?
  • We need to define/narrow the topic to cover in one hour
  • What are common/different annotations captured by DBs? What data model/infrastructure changes would be required to come to common ground?
  • Paul S. will discuss with Karen and Doug about topics

June 16, 2016

SimpleMine on WB frontpage?

  • Wen has asked to put it under the Tools menu

Curating phenotypes to complex genotypes

  • Should we objectify phenotype experiments, much like ?RNAi objects
  • This would allow encapsulation of genotype elements and phenotype info
  • Curators could explicitly state causative gene in a transgene, but keep automated mapping for RNAi, alleles, and rearrangements
  • Chris will work on data model
  • This may mean we want to eventually merge the Phenotype OA and the RNAi OA

Datomic queries

  • Variation not currently connected to phenotype
  • Matt R. is working on it

June 23, 2016


NOTE: this meeting is the C. elegans Development, Cell Biology and Gene Expression Topic meeting.

  • we will be at a shared booth with Flybase and SGD


  • Room for one poster at SGD/FB/WB booth
    • Large scale gene expression (SPELL) + Pathways


    • Community annotation + Micropublication
    • Projector in the shared booth - can bring a slide deck
    • Need to come up with the AGR unified poster
  • One poster for MOD Demo room - will be a table, easel for displaying poster (2nd poster)
  • Paul, will you be presenting a poster during the normal poster session? Can bring it to the Demo room for further display and demo textmining


  • bags from past IWM - how many, how would we get them to Orlando - Sarah ships them?
  • SGD will have bottle openers
  • tattoos?
  • special gifts? SGD will have hats (50); do we have any fly swatters left? If so, how many?
  • coloring book publishing

Automated descriptions

  • Michael and Ranjana fixed the pipeline for orthology (was missing many orthology statements)

Citace upload

  • Next Tuesday (June 28) 10am

Disease annotations

  • Most disease info currently captured as gene-to-disease connections
  • Ranjana may want to create disease annotation objects in the database
  • Could be modeled similarly to GO annotation objects
  • Will help to encapsulate the data into one object per experiment in a paper, for example

Phenotype report objects

  • Want to capture complex genotypes, zygosity, RNAi with multiple targets, etc.
  • Chris proposing a potential new "phenotype report" class to subsume RNAi objects and allele- or transgene- phenotypes
  • Would require many changes to mapping and build pipeline adn data display, so need to discuss issues with Hinxton and OICR

Evidence Code Ontology (ECO)

  • Would be worth considering adopting ECO or similar evidence code system
  • Kimberly: there is an experimental factor ontology, and OBI (ontology of biomedical investigations)
  • Raymond: XCO, experimental condition ontology

Community petition for MOD support

  • GSA and fly board put together a letter to NIH with signatures
  • Would be good to link to the letter from WB homepage
  • Ranjana will create blog post

June 30, 2016

Virtual Worm images on anatomy pages

  • Daniela, Raymond, Chris working on importing existing cell and anatomy object images into WB anatomy pages
  • There are currently no images of tissues/cells on each page
  • We have links to WormAtlas but not their images
  • Virtual Worm cells and cell groups have already been rendered

Citpub on Spica

  • Testing instance of citpub ACEDB, single instance to be shared (cannot be used by multiple users simultaneously)
  • People can create their own instance for ACEDB testing
  • If someone else is already running citpub ACEDB, people can read but not write (when reading in .ace files for testing)

Proteomic paper data

  • Wen has been looking at proteomics papers
  • She's been looking for "proteome" in titles and journal names, "SILAC" technique in whole text
  • Already curated 31 expression cluster proteomics papers
  • 39% precision, 61% recall (183 new papers)
  • Tried "LC-MS" but was too non-specific
  • Wen has worked with Gary Williams to identify mass-spec papers
  • Will ask Yuling about any paper flagging pipelines

Phenotype curation interface call yesterday

  • ZFIN curates via the ZFIN site (after logging in) and data goes live immediately
  • ZFIN uses spatial ontology to specify regions of anatomy or cell affected by phenotype
  • ZFIN and RGD build phenotype annotations by selecting terms and sending them to a phenotype "bucket"
  • RGD includes disease annotations in parallel to phenotype annotations (connecting rat, mouse, and human)
  • RGD captures detailed numbers

Phenotype report objects

  • Chris considering a change to phenotype data model to capture phenotype report objects
  • We will surely want to capture differential phenotypes and differential genotypes
  • We will need to consider if we want to (and how to) capture absolute phenotype measurements
  • Objectifying phenotype annotations may be similar to the Monarch phenopacket model
  • Karen has communicated with Chris Mungall about including anatomy, molecule, lifestage information in the phenotype association file that he can use to map Worm Phenotypes to Human phenotypes.

RGD paper lookup

  • RGD curators lookup phenotype and related terms and use OntoMate to lookup papers with that information
  • Looks similar to Textpresso Central lookup; not sure if they have access to full text or just abstract