Florian Gräf Genes genomes amp variation ArrayExpress Expression Atlas Metabolights PRIDE InterPro Pfam UniProt ChEMBL ChEBI Literature amp ontologies Europe PubMed Central Gene Ontology ID: 804465
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Slide1
Implementing the Joint Data Citation Principles in JATS for core life sciences data resources
Florian
Gräf
Slide2Genes, genomes & variation
ArrayExpress
Expression Atlas
Metabolights
PRIDE
InterPro
Pfam
UniProt
ChEMBL
ChEBI
Literature & ontologies
Europe PubMed Central
Gene Ontology
Experimental Factor Ontology
Molecular structures
Protein Data Bank in Europe
Electron Microscopy Data Bank
European Nucleotide Archive
1000 Genomes
Gene, protein & metabolite expression
Protein sequences, families & motifs
Chemical biology
Reactions, interactions & pathways
IntAct
ReactomeMetaboLights
Systems
BioModelsEnzyme PortalBioSamples
Ensembl Ensembl Genomes
European Genome-phenome ArchiveMetagenomics portal
EBI-Services Landscape
Slide3Europe PMC
Partner of PMC International30M abstracts
including
PubMed, 3.5M full-
text articlesManaging the EMBL ORCID integrationOpenAIRE and THOR contributer
Slide4http://
europepmc.org/articles/PMC3710810
Fig. 2
Slide52/3/2016
5
Slide6Our Route to Data Citation
Data-Literature Integration
Force11 meeting Amsterdam
Text mining accessions
JATS v1.1: Data citation extension
OpenAIRE
THOR
Photo by
James,
Wheeler; “Yoho Road” [http://www.souvenirpixels.com/photo-blog/yoho-road.html]
Slide7OpenAIRE 2020
Task 7.3 – Data-Literature IntegrationEvaluation of status quo and how to improve itWhat does data citation look like nowTo what degree can the DCP be satisfied today?
How can data literature links be presented?
How can they be machine readable?
Implementing DCP in JATS v1.1
Building a proof of concept tool providing JATS xml from accession and database nameContribution to the Data-Literature interlinking service
Slide8F11 DCP Compliance
Evaluated
Metadata
ENA
PDB
Samplesize
Open Access set
from EuropePMC text
mined accessions
70k16.5k
Credit, Attribution
Data Repository, Submitters~94%
100%Unique
Identification, Access, PersistanceAccession100%100%Specificity,
VerifiabilityVersion, (Modifiaction Date)100%~49.2%Overall
All above~98%~83%
Interoperability and Flexibility fulfilled by JATS XML FormatNo versions
Slide9Accession2Jats Prototype Workflow
Input
Repository: PDB
Accession: 3g76
Retrieve metadata from public API
Slide10JATS 1.1 Data Citation Example
Slide11Accession2Jats Prototype Workflow
Input
Repository: PDB
Accession: 3g76
Retrieve metadata from public API
XSL-Transformation
Cossu
F., Milani M.,
Mastrangelo
E.,
Bolognesi
M. (27 Oct
2009). Crystal structure of XIAP-BIR3 in
complex with a bivalent compound. PDB 3g76 [
http://www.ebi.ac.uk/pdbe/entry/pdb/3g76].
Slide12And now?
Complete PrototypeGithub: FlorianGraef/acc2jats
Work
with publishers to incorporate tools into workflows
graf@ebi.ac.uk