WormBase-Caltech Weekly Calls September 2014

September 4, 2014

I need to leave at 5.30pm (ermm, 9.30am CA time?) Mary Ann

Concise Descriptions

• Automated descriptions to go in for WS245

New Upload Schedule

• Delayed a couple weeks compared to original schedule
• Official citace upload to Hinxton on October 10th
• We can/should upload our data Wednesday before SAB trip (October 1st) to Hinxton
• Wen needs queries to include in Citace Upload summary by October 1st
• Upload contingent on models freeze

Data submission as part of publication process

• eLife considering micro-publication, addendums to papers (individual add-on experimental results)
• Can certain data be required to publish? Sequence info, etc. ?
• Could there be a pilot with a specific publisher (like GSA markup)?

Elixir

• http://www.elixir-europe.org/
• Use RDF (Resource Description Framework) triples
• Checking individual statements/sentences from literature for data presence/absence in database

New tags in Qualifier Hash

• Life_stage and Anatomy_term
• Adding to enable annotation of EPIC data
• Couples (or attempts to) time-and-space (life_stage-and-anatomy) annotation of expression pattern
• Can ambiguities be captured?
• This approach (bit of a kludge) introduces some denormalization (normalization can be automated later)

LEGO Curation

• Setting up connection to Minerva
• Juancarlos working with Seth, Chris, Heiko to debug setup
• Would be good (necessary?) to establish a working protocol for collaboration
• Raymond's LEGO-like approach to curating anatomy function
  • Annotate a phenotype by annotating relevant DB objects, e.g. anatomy term, GO term, etc. as well as context/condition
  • Use minimal relationships (relationship ontologies complicated and difficult to use)

September 11, 2014

SAB Meeting

• Can we start putting together a more detailed agenda, at least for Caltech?
• Would be good to decide on our talk topics so we can begin putting our presentation(s) together.
• Curation Stats numbers spreadsheet
  • Good to capture amount of time (FTEs) on curation, but also software development, curation tools, pipelines, data modeling, help desk, fixing old data
• Would be good to have a rough breakdown of every curator's FTE breakdown
• Allocation of resources
• Ontology development; how much time is spent? Is it worth it?
• What tools do we have, or could we develop, that could substantially improve efficiency/effectiveness of curation? Example: sequence generation tool
• What are considerations for future database migration? We should account for migration delays to curation, etc.
• The curation database (like Postgres now) may or may not be the same database that drives the website
• Are our curation pipelines capturing sufficient detail (or too much, unnecessary detail)?
• Is it worth capturing negative data?

SAB Talk Proposals

• Nomenclature - not stats, but what we do, how it's done, communication etc Mary Ann
• Sequence Feature - developments Mary Ann
• Physical Interaction Curation - a relatively new data type for us, discuss existing data, strategies for going forward, what groups we could/do collaborate with, what files we could provide
• Community-Assisted Curation - what we currently do (author first pass, data submission forms), what more we could do (CANTO)
• Topic-Based Curation

September 18, 2014

Epic Data

• Daniela will test once Paul tags models (tomorrow Friday Sept 19th, 2014) and then upload to citace minus
• Wen needs a couple days from model tagging to prepare the final upload

SAB

• Chris (Caltech curation overview)
  • Pipeline/Mission of Caltech (pull biological data from papers and put into database)
  • Curation data types
  • Who is who, who does what? (Photos of curators?)
  • Curation stats, what is up to date, what needs more effort?
  • Rate-limiting steps, tools (OA, curation status form, etc.) (slide from Daniela)
  • Topic curation, pathways curation
  • Brief statement on curation of other nematode species
• Wen (Expression Clusters)
  • Couple slides on expression curation from Daniela
  • What are expression clusters? Come from microarray, proteomics, tiling array
  • Triage, pattern matching
  • SPELL tool: what is it? usage?
  • Display of expression cluster data
  • WormBase generated expression clusters (custom algorithm?)
  • Enrichment of GO terms and anatomy terms (segue into WOBr talk)
• Raymond (WormBase ontology browser)
  • We use and develop a number of ontologies
  • The ontological structure allows hierarchical browsing and reasoning
  • Co-opting Amigo2 (existing tool)
  • OWL formats
  • Future developments
• Mary Ann (Nomenclature & Sequence features)
  • Sequence features
    • Sequence feature data display
    • JBrowse/GBrowse integration
  • Nomenclature
    • CRISPR alleles
• Ranjana (Human Disease)
  • Update
  • Two classes of disease models: Genes (via variations) & transgenes (overexperssion, deleterious repeats, etc.)
  • ~260 gene models for human disease
  • Drugs & therapeutic compounds, metal toxicity (toxicology in general)
  • Disease portal? Toxicology portal?
  • Toxins in Textpresso?
• Kimberly (GO curation)
  • Enrichment analysis
  • Priorities for GO
  • Annotation extensions & LEGO curation

September 25, 2014

SAB Preparations

• Review of overview presentation
• What data are we not curating from the newest elegans/nematode papers?
  • Papers per year is roughly flat per datatype per year but total number of papers is going up ~10% each year
• How many minutes should each CIT curator get to present?
• Karen will present Process/Topic slides (take over from Chris)
• Chris - Curation Overview, Ranjana - Disease, Raymond - WOBr, Wen- Expression datasets, Kimberly - GO, Mary Ann - Nomenclature, Sequence

New Backups

• Raymond setup backups through Duplicity
• Tazendra, Mangolassi, Athena, Canopus, other Linux machines backed up
• Backup is limited to two years; any data removed from a machine earlier than 2 years ago will be lost

Sequence Feature OA

• Currently read only, makes data available to curators
• Populated OA on sandbox (Mangolassi); skeleton form on Tazendra