Publication criteria and contributor credit

1. Publication criteria and contributor credit HVP Paris 14th May 2010

2. HVP/UNESCO Press release 14th May Funders of research into human genome variation must require a plan for data sharing and annotation and provide funds for data integration activities. Mandatory data release is necessary but not sufficient for use in research and in healthcare decisions. Data need to be curated to agreed standards, and to be integrated and harmonized. The long-term sustainability of this curation work should also be discussed in the emerging ESFRI framework in Europe and similar initiatives worldwide. Contributions to this collaborative annotation work can be recognized by unique contributor-controlled identifiers such as ORCID (www.orcid.org). We endorse closer collaboration of groups working on semantic interoperability using concept web (semantic web) approaches for life sciences.

3. Required HVP actions Develop a protocol for variant submission to databases that will enable publication and attribution [Editors’ resolution, Café RouGE] Standardize citation of molecular resource IDs [Editors’ resolution, BRID, OID, CWA] Standardize clinical reporting [Journals that do this please explain, BRID, ICD-11] Identify unique authors using ID controlled by the authors themselves (ORCID) and publish contributor roles (eg. author, curator, consortium member) [Participants involved in these projects please identify funding and roles]

4. Speakers’ main points Jean-Jacques Cassiman www.eurogentest.org As incentives to deposit variants to databases, clinical testing labs might be required as condition of accreditation or certification to submit properly formatted variants together with biochemical, molecular or clinical information. Processes for evaluating genetic tests: http://www.cdc.gov/genomics/gtesting/ACCE EGAPP process for evaluation of genetic tests for clinical practice http://www.egappreviews.org/ Establishing an ISO norm takes a long time, there is one registered for variants: Human genome variation markup language ISO 25720:2009 Joseph Borg Hemoglobin variants have been collectively annotated in a Human Variome Microattribution Review together with MeSH phenotypes, frequency, geographic origin in HbVar and LOVD databases, giving citation credit to the original observers and the curators. After publication, can this data be represented on a wiki browser to collect comments and future variant reports, can this also collect Concept Web RDF nanopublication constructs? Gudmundur Thorisson You already have an OpenID. ORCID is being developed by agreement between a large number of stakeholders but ownership by individuals is not yet assured. ORCID group should not be slowed down by having to take contributor roles into account but we will need to consider how to implement this. G2P wiki is available for comment http://www.gen2phen.org/wiki/ Gabrielle Bertier Bioresource IDs will be piloted in BBMRIhttp://www.bbmri.eu/ under Gen2Phen. Quantitative citation of BRIDs will be monitored to report a bioresource impact factor. Can BRIDs be DOIs and harmonized with Datacite? Are research participant IDs with public and private components feasible? Ségolène Aymé ICD-10 is “a disaster for rationality” and is too organ-centric. ICD-11 is system based, takes into account multisystem diseases and provides better distinction between constitutional and acquired disorders. Although ICD-11 will be published in 2014, it will be finalized shortly, so users should comment NOW http://www.eucerd.eu/

5. Each Cardinal Assertion maps to three UUID’s • ARTA table enables mapping across URI’s • Three UUID’s (subject-predicate-object) form new UUID for CA • Computer Reasoning uses Cardinal Assertions + evidence weight S p Also Referred To As ..ARTA o Inferencing Association CA1 CA2 CA3

6. CWA and semantic web integration Barend Mons There is plenty of room at the bottom. UUIDs and RDF provide the Concept Web with sufficient identifiers to make semantic triples for most biological assertions. The Large Knowledge Collider LarKC can reason across 20bn such constructs in a day for about 1k Euros. Amazon cloud provides sufficient storage. LSDBs and other databases should make sure that all tokens and identifiers they chose to use internally to denote concepts , such as genes, variants, diseases, tissues etcetera (whether they are terms, identifiers or URI's) are in the ARTA table of the public concept wiki or connected to the Knowledge enhancer. This way, all assertions in the LSDB or any other database can be 'exposed' to the concept web and are now part of massive analysis, such as LarKC All contributors, submitters as well as curators should author-ize their page in the conceptwiki, and add all tokens (such as spelling variations, scopus ID, etc. to their ARTA table if not yet already there. When ORCID, CrossRef, VIVO, Datacite and other organisations can resolve each of those tokens referring to the contributor to the UUID, all contributions will be micro-attributed to the contributor and will be visible on the contributors page as nano-publications.  All 'impact' calculators can use this public wiki to compute individual contributions and give credit.

7. What conventions and accession codes do 8 journals enforce? Myles Axton Annals of Human Genetics, Genetics in Medicine, Genome Research, Human Mutation, Journal of Human Genetics, Journal of Medical Genetics, Nature Genetics, PLoS Biology Grant and funder information 6 by initials, 3 optional Competing financial interests 5 publish, 1 if positive, 2 optional OMIM accession 4 mandate, 4 do not HGNC gene names 4 throughout, 3 first use, 2 no obligation Model organism database: genes 4 mandate mouse, 3 all models DNA sequence 4 public deposit, 2 encourage, 2 no obligation Primer sequences 4 mandate publication, 4 no obligation Expression array 3 mandate, 2 encourage, 3 no obligation LOVD deposition of human variants 3 endorse, 5 not policy Prepublication data sharing 2 for review, 1 if referees, 1 no enforcement, 4 no policy Postpublication data sharing 2 enforce, 1 policy, 5 no policy NCBI/EBI deposition of human variants 2 mandate, 3 endorse, 3 not policy Author contribution statement 2 by initials, 4 optional, 1 in supplementary information HGVS allele nomenclature 1 throughout, 1 first use, 2 optional, 4 no policy

8. Editors’ draft resolution of support for community databases Myles Axton, Theodora Bloom, Mark Paalman, Giuditta Perozzi General If there is a public repository used by the community that offers unique accession codes and bidirectional linking via the article identifier, we will insist upon deposition as a condition of peer review. We will monitor citation of the data accession and offer quantitative use data. If the database or journal receives little traffic via the link, we may terminate the linking arrangement. Specific We will endorse HGVS nomenclature and expect that each variant description will correspond to a unique database entry where all reports about that variant will be aggregated. That page can be bidirectionally linked via all the article identifiers of the papers that cite the variant.

9. No compulsion without incentive