The journal as index and incentive for data publication

Myles AxtonEditor, Nature Genetics

CambridgeOct 23rd 2011

Nature quality primary research in genetics and genomics

- Professional editors choose which papers to publish

- Peer referees provide technical guidance to improve the work

- Editorial standards and decision criteria are constantly revised in light of referee advice, author comments, conference presentations and lab visits

- Standards of the journal constantly get higher

All Nature Research Journals use two basic criteria for decisions:

Novelty: new data, new resource

Conceptual advance: new ideas, new strategies

Plus:

Nature: Is this work of general interest to all scientists, to decision makers or to the public?

Nature Genetics: How many other researchers will do their research differently as a result of this work?

Scope of Nature Genetics

Common/complex diseases - RiskGene networks - Wiring

CancerHuman disease geneticsPharmacological genomicsEpigeneticsDevelopmental geneticsFunctional genomicsStem cell geneticsGenetic technologyGenome evolution

Results, data, funding and contributors

Footnotes and XML tags for contributor roles

Publisher metadata transmitted to popular sites

Better information and metrics for authors and funders

Citable data management plans by data producers

- Citable by unique digital object identifier (DOI) that points to current version.

- Previous versions stored and independently citable.

- Project descriptions (“marker papers”) grouped in a Collection together with funder policy documents and community standards papers.

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: 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

Pilot study in data publishing and citation

Thomson ReutersJoel HammondBruce Kiesel

NPGMyles AxtonTony Hammond

Penn. State U.Belinda Giardine

Erasmus Med. Cent.Bharat Singh

Free U. AmsterdamPaul Groth

Leiden U. Med. Cent.Herman van HaagenErik SchultesBarend MonsIvo FokkemaJohan den Dunnen

Microattribution

Journals provide citation links from paper to paper. Quantitative citation provides a rough measure of usefulness.

Database accessions should be traceable to their original source.

Citations to database accessions in peer reviewed papers and in database entries should be counted and the count made public.

Microcitation provides incentive for collaborative genome annotation and a more accurate picture of individual and group research activity.

Microattribution can be extended to web traffic analysis.

Microattribution is an incentive to database deposition

Microattribution started

Human Variome Microattribution Review (Hemoglobin)

http://www.bx.psu.edu/~giardine/

RDF/XML triplet with provenance metadata

Supplementary Table 1 Nanopublications of the form [HGVS gene variant name][has][Variant frequency]

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"    xmlns:n="http://example/schema/">  <n:nanopublication rdf:about="#2000">    <n:triplet>      <rdf:Statement>        <rdf:subjectrdf:resource="http://example/id/NG_000007.3:g.70628G>A"/>        <rdf:predicaterdf:resource="http://example/genetics/has-variant-frequency"/>        <rdf:object>0.25%</rdf:object>      </rdf:Statement>    </n:triplet>    <n:condition>Sardinian</n:condition>    <n:provenance>      <rdf:Description>        <n:researcherID>HbVar (A-2391-2010)</n:researcherID>        <n:DOI rdf:resource="http://dx.doi.org/10.1038/ng.785"/>        <n:PMID rdf:resource="info:pmid/6695908"/>        <n:PMID rdf:resource="info:pmid/1428944"/>        <n:PMID rdf:resource="info:pmid/1610915"/>        <n:linkoutrdf:resource="http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&amp;display_format=page&amp;i=239;http://phencode.bx.psu.edu/cgi-bin/phencode/phencode?build=hg18&amp;id=HbVar.239"/>      </rdf:Description>    </n:provenance>  </n:nanopublication></rdf:RDF>

Our experiments suggest articles are a poor source of data

Leiden Open Variation Database (LOVD)196,000 variants in 3,267 genes from 84,937 individuals Giardine et al. (ng.785) 1,901 unique variants in 37 genes affecting hemoglobin levels

1) Text search 10m PubMed abstracts with 4,940 gene variants of 11 genes in LOVD.

16 out of 10,000,000 abstracts contained gene variants from the search set

2) Search for 2,545 DMD variants in the full text of 109 articles on Duchenne muscular dystrophy selected by LOVD curator Johan den Dunnen.

625 out of 2,545 variants were found in 22 out of 109 articles (2,565 total mentions)

3) Search all LOVD entries with PubMed PMIDs indicating Nature Genetics articles.

LOVD database linked a gene variant to 19 of 36 articles. Only 3 articles mention the variant in unambiguous HGVS nomenclature in the text.

4) Text mining ng.785 for nanopublications concerning all biomedical concepts.

a) From the article, 13 out of a total of 698 nanopublications assert genetic variation

b) From the Supplementary Tables, 1,734 nanopublications of the form [HGVS variant][has][OMIM VarID]

and 121 of the form [HGVS variant][has][variant frequency]

c) >40,000 nanopublications from the HbVarDB described by the article

Scholarly communication

Current Proposed

Nature Genetics 43, 281–283 (2011) doi:10.1038/ng0411-281

Thank you!