1. Implementing the Joint Data Citation Principles in JATS for core life sciences data resources
Florian Gräf
Software Developer of the McEntyre group at EMBL-EBI
Working on:
Europe PMC
ORCID integration
THOR
OpenAIRE

2. EBI-Services Landscape
Genes, genomes & variation
ArrayExpress
Metabolights
Expression Atlas
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
Reactome
MetaboLights
Systems
BioModels
BioSamples
Enzyme Portal
Ensembl
Ensembl Genomes
European Genome-phenome Archive
Metagenomics portal
Core Services at EBI
But there too are many research groups
EuropePMC one of many services at EBI

3. Europe PMC Partner of PMC International
30M abstracts including PubMed, 3.5M full-text articles
Managing the EMBL ORCID integration
OpenAIRE and THOR contributer

4. Fig. 2 http://europepmc.org/articles/PMC3710810 Why do we do this?
What does Data citation (often) look like

5. 11/27/2018 Why did we start text mining?
- We are interested in the context of data mentions/ data citations
- Accessions are often not tagged by publishers
11/27/2018

6. Our Route to Data Citation
Data-Literature Integration
OpenAIRE
THOR
JATS v1.1: Data citation extension
Text mining accessions
Data tagging in publications? Often poor or non existent
So better Data-Literature Integration is the goal
Jee Hyub learned about F11 DCP at a Force11 meeting in Amsterdam
-> Start text mining accessions
We contributed to the datacitation integration in JATS in v1.1
Engagement in OpenAIRE (data-literature integration) and THOR
Force11 meeting Amsterdam
Photo by James, Wheeler; “Yoho Road” [

7. OpenAIRE 2020 Task 7.3 – Data-Literature Integration
Evaluation of status quo and how to improve it
What does data citation look like now
To 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 name
Contribution to the Data-Literature interlinking service
Status quo.
what does dc look like? We have seen this

8. F11 DCP Compliance
Evaluated Metadata
ENA
PDB
Samplesize
Open Access set from EuropePMC text mined accessions
70k
16.5k
Credit, Attribution
Data Repository, Submitters
~94%
100%
Unique Identification, Access, Persistance
Accession
Specificity, Verifiability
Version, (Modifiaction Date)
~49.2%
Overall
All above
~98%
~83%
No versions
Evaluation
Interoperability and Flexibility fulfilled by JATS XML Format

9. Accession2Jats Prototype Workflow
Input
Repository: PDB
Accession: 3g76
Retrieve metadata from public API

10. JATS 1.1 Data Citation Example

11. Accession2Jats Prototype Workflow
XSL-Transformation
Input
Repository: PDB
Accession: 3g76
Cossu F., Milani M., Mastrangelo E., Bolognesi M. (27 Oct 2009). Crystal structure of XIAP-BIR3 in complex with a bivalent compound. PDB 3g76 [
Retrieve metadata from public API

12. And now? Complete Prototype Github: FlorianGraef/acc2jats
Work with publishers to incorporate tools into workflows
Contact me with feedback, suggestions
Next steps: we are interested in working with publishers regarding how to incorporate potential tools based on what I just described into workflows.