Crossref’s view of the - Council of Science EditorsPreprints - Crossref’s view of the expanding...

Jennifer Lin, PhD@jenniferlin15orcid.org/0000-0002-9680-2328

CSE 2018, 8 May 2018

Preprints - Crossref’s view of the expanding territories

Crossref - scholarly infrastructure• Founded to fight link-rot and ensure that the citation record is

clear and up-to-date, functioning consistently across publishers

• The metadata is useful, freely available, human & machine accessible

• Works are connected to the full history of the published results• Contributors are given credit for their work (ORCID)• Everyone can identify the provenance and get context of a

work

DOI DOI

DOIDOI

DOI

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Metadata:

Literature Associated research outputs

Associated research entities

Article

Associated research entities

• authors• collaborators

• reviewers• editors

• funders• affiliations

Literature

• datasets• software

• protocols• materials

• preprints• conf papers

• peer reviews• translations…

Associated research outputs

Article

Literature

42,541 preprints

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Date registered

Yr and a half ago 1yr ago Half a yr ago This month

Volume of registered preprints in Crossref

Jordan Anaya, PrePubMed http://www.prepubmed.org/monthly_stats/

Preprints by publisher (May 5, 2018)• bioRxiv: 24,571• PeerJ Preprints: 8,974• Preprints.org: 4,211• JMIR Preprints: 2,090• ChemRxiv: 729• Therapoid (Open Therapeutics): 2

Preprints metadata• Repository name & hosting platform• Contributors & ORCID• Title• Dates (posted, accepted)• License• Funding• Abstract• Relations• References

Metadata currently depositedOut of 42,541 records, the following metadata have been registered:• License: 9710, 23% (PeerJ Preprints, ChemRxiv)• Funder: 0, 0%• ORCID: 18239, 43% (bioRxiv, PeerJ Preprints,

Preprints.org, ChemRxiv)• Abstracts: 34508, 81% (bioRxiv, PeerJ Preprints, ChemRxiv)• References: 1740, 4% (JMIR) Crossref REST API

api.crossref.org

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Metadata deposited (all Crossref records)

12,983 articles published from preprints

10.20844/preprints201608.0191.v1 is a preprint of10.3390/data1030014

“Hey Crossref, which papers in my journals have preprints?” Let me check

the REST API…

Let me check the Citedby count in the REST API…

“Hey Crossref, what are my most cited preprints?”

It’s all about relations:relationship types connect the article with its resources

Research nexus: ClusterflockClusterflock: an algorithm optimizing distance-based clusters in orthologous gene families that share an evolutionary history• Paper: https://doi.org/10.1186/s13742-016-0152-3• Preprint: https://doi.org/10.1101/045773 • Supporting data: http://dx.doi.org/10.5524/100247 • Code: https://github.com/narechan/clusterflock • Docker hub: https://hub.docker.com/r/narechan/clusterflock-0.1 • Video demo: https://youtu.be/ELZTVOiqKn8 • Peer reviews: https://doi.org/10.5524/review.100507 and https://

doi.org/10.5524/review.100508

Article

• shares• mentions

• discussions• citations

• recommendations• reviews…

Activities surrounding itLiterature

Most highly cited preprints1.Citedby 71 - https://doi.org/10.1101/005165 qqman: an R package for visualizing GWAS results using Q-

Q and manhattan plots. May 14, 2014. 2.Citedby 63 - https://doi.org/10.1101/002824 HTSeq - A Python framework to work with high-throughput

sequencing data. August 19, 2014. (10.1093/bioinformatics/btu638, 2288 citations) 3.Citedby 43 - https://doi.org/10.1101/030338 Analysis of protein-coding genetic variation in 60,706

humans. May 10, 2016. (10.1038/nature19057, 1518 citations) 4.Citedby 38 - https://doi.org/10.1101/002832 Moderated estimation of fold change and dispersion for RNA-

seq data with DESeq2. November 17, 2014. (10.1186/s13059-014-0550-8, 3168 citations) 5.Citedby 28 - https://doi.org/10.1101/021592 Salmon provides accurate, fast, and bias-aware transcript

expression estimates using dual-phase inference. August 30, 2016. (10.1038/nmeth.4197, 103 citations) 6.Citedby 21 - https://doi.org/10.1101/012401 DensiTree 2: Seeing Trees Through the Forest. December 8,

2014. 7.Citedby 21 - https://doi.org/10.1101/011650 FusionCatcher - a tool for finding somatic fusion genes in

paired-end RNA-sequencing data. November 19, 2014. 8.Citedby 18 - https://doi.org/10.1101/006395 Error correction and assembly complexity of single molecule

sequencing reads. June 18, 2014. 9.Citedby 18 - https://doi.org/10.1101/032839 Spread of the pandemic Zika virus lineage is associated with

NS1 codon usage adaptation in humans. November 25, 2015. 10.Citedby 17 - https://doi.org/10.1101/048991 Analysis of shared heritability in common disorders of the

brain. September 6, 2017.

• Funders• Institutions• Archives & repositories• Research councils

• Publishing vendors• Metrics providers• Reference manager systems• Lab & diagnostics suppliers

• PID providers, registration agencies

Crossref metadata reaches:

• Data centers• Professional networks • Patent offices• Indexing services

• Sharing platforms• Data analytics systems• Literature discovery services• Educational tools

Thank youJennifer Lin, PhDjlin@crossref.org

@jenniferlin15orcid.org/0000-0002-9680-2328