Community Curation at

o  History o  Requirements for easy to use Curation tool

(Canto ) o  Results, numbers of papers & annotations o  Curation Quality o  How we Motivate the community o  Lessons learned

History Rationale: o  Need to be sustainable with increasing data and static

(or reducing) funding o  Authors should be the best people to interpret *their own data* o  Support funding bid Proof of principle (pilot 2009): o  35/49 publications assigned to lab heads curated using

a form o  71% participation (after 3 reminders) o  >600 annotation More background: http://www.pombase.org/community/fission-yeast-community-curation-project

o  Use by professional curators and community o  Web based o  Generic (configurable for any organism) o  Ontology based o  Publication centric o  Provide triage facility (admin) o  Literature and curation session management (admin) o  Easy to use (no curation background required)

Curation Tool Requirements

Canto was developed by Kim Rutherford at PomBase

Step by step …. Add PMID …. Add genes …. Select gene …. Select data type …. Find term …. Add evidence, extensions, Repeat for each gene/experiment

Simple Workflow

Canto Demo https://youtu.be/dmDtpDjNMSk (video demo)

Results:Participation

New curators/yr. (non cumul.)

1147 papers assigned 410 returned, Response rate 36 % Generated 7766 annotations

Users generating >100 annotations Shown on PomBase front page

ExcludesHTPdatasetswhichcomeviaotherroutes(spreadsheets)

Annotations/yr

Results:Paper/curation #s

Papers curated by date of publication

•  The community are curating recent papers •  These contain more data

Results:Paper/curation #s

By year of publication (note: all curated since 2012 using same criteria)

(Excludes HTP datasets)!

Curation quality o  Annotation Completion 5-100% (avg.~50%) Often omit a data-type – added by PomBase o  Term Specificity usually ~95-100% (more likely to see a more specific term request) o  Term Accuracy ~95-100% (less experienced will add GO for indirect phenotypes) o  Noticeable improvement for subsequent papers o  Most sessions involve dialogue with author to refine (QC) o  PomBase curator’s annotations are checked and

corrected if necessary by author

Community Motivation o  Participation encouraged via mailing list (1200 members) o  PomBase 15,000 unique users per/month …increased visibility, more citations o  Data propagated to GO, UniProt, NCBI, BioGRID o  All post 2013 papers not processed until community

session received o  Increases community knowledge of data representation/

available terms. Improves use in data-mining, analysis o  Attribution using ORCID towards satisfying funding

bodies data dissemination requirements

PomBase curation requirements are very detailed (high expectations……) o  Kilchert Vasiljeve lab http://tinyurl.com/zc6hqyn (extensions

~200 annotations) o  Pluskal Yanagida lab http://tinyurl.com/q2bgyqv o  Nakamura http://tinyurl.com/zqd8a6m (all data types,

extensions) o  Watanabe http://tinyurl.com/jjqzzw3 (extensions on

phenotypes) o  Gould http://tinyurl.com/o72bzul (GO, phenotypes,

extensions) o  Toda http://tinyurl.com/p7d979b

Example sessions

Lessons learned o Postdocs and grad students keen to curate

their papers o People need to be asked (invitation, link to

curation session) o Recent paper, more likely to be curated o Reminders are often required o Curators need to check sessions (QC) o Noticeable improvement for subsequent

papers

Future o  Implement an organism independent GO only

version? o  Attribution via ORCID, OpenRIF? o  Aim to reach 50% of all curation via this route

by 2019 o  Term suggestions (you may want to…)

o  Model organism databases: essential resources that need the support of both funders and users

o  http://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0276-z

o  PomBase curation stats https://curation.pombase.org/pombe/stats/annotation

o  Canto Demo Tool https://curation.pombase.org/demo

o  Canto Demo Video https://youtu.be/dmDtpDjNMSk

Links

The PomBase team Kim Rutherford (developer ) Cambridge University Midori Harris (curator and FYPO developer) Cambridge University Antonia Lock (curator) UCL Valerie Wood (curator, project manager) Cambridge University Jaqueline Hayles (community curator) Crick Institute Steve Oliver (PI) Cambridge University Jurg Bahler (Co-PI) UCL

Acknowledgements