Publication criteria and contributor credit

1. Publication criteria and contributor credit Myles Axton Editor, Nature Genetics HVP 12th May 2010

2. What conventions and accession codes do 8 journals enforce? 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: gene names 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

3. Editors’ resolution of support for community databases 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.

4. Required HVP actions Develop a protocol for variant submission to databases that will enable publication and attribution [Editors’ resolution] Standardize citation of molecular resource IDs [Editors’ resolution] Standardize clinical reporting [Journals that do this please explain] 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]

5. No compulsion without incentive

6. Precise citation credit for combinations of database accessions A) URI/OpenURL convention can be used to give credit to contributors as well as to find unique resources on the web (its current role) B) A citation vector is a set of accession codes listed in the parameters of a URI: 1) contributor=MyDB.Jane_Doh seq=ss456 pheno=phs5.v2.p1 published=DOI.12 2) contributor=DOI.12_authorlist seq=ss716 array=Illumina1M citedby=DOI.34 3) contributor=BIG_Consortium transcriptome=GSE078 citedby=ss456 C) The contributor parameter resolves the URI to an entry in the citation repository that can credit each vector to a set of contributor IDs because it stores consortium membership (with dates) and author lists D) Repository keeps track of the authority and namespace for relevant accession code types (eg. pheno=phs5.v2.p1 is a NCBI/dbGAP phenotype accession, version 2) E) Quantitative microcitations to database accessions in peer reviewed papers and in database entries can be obtained from the citation repository: As with CrossRef, everyone has access to the same citation information. Microattribution can be extended to web traffic analysis F) Data multiples can be used in Concept Web (semantic web), combined with concept multiples G) Public unique reference. This new type of accession code indicates further confidential data is available upon Data Access Committee approval. Allows credit to patient group or clinic. Can be decoded from patient side