Biotea is a semantic dataset that RDFizes (converts to RDF) the open-access subset of PubMed Central. It makes scholarly documents and their metadata interconnected by extensively using existing ontologies and semantic enrichment services. This allows the generation of machine-readable scholarly documents that are self-describing. The Biotea dataset and tools provide a flexible and adaptable way to semantically enrich and process biomedical documents into a highly interconnected and semantically rich dataset.

1. Biotea: RDFizing PubMed Central in Support for the Paper as an Interface to the Web of
Data
Alexander Garcia, Casey Mclaughlin,
Institute for Digital Information,
Florida State University. Tallahassee
Leyla Garcia Castro
Departamento de Leguajes y Sistemas Informáticos
Universitat Jaumé I
Corresponding author: alexgarciac@gmail.com
Scholarly data and documents are of most value when they are interconnected rather than independent
Christine L. Borgman
In a nutshell, Biotea at http://biotea.idiginfo.org
• Is a semantic dataset for full-text, open-access subset of PubMed Central
• Makes extensive use of existing ontologies and semantic enrichment services
• Supports the generation of self-describing machine- readable scholarly
documents.
• Comprises a flexible and adaptable set of tools for metadata enrichment and
semantic processing of biomedical documents.
• Provides semantically rich and highly interconnected dataset with self-describing
content.
RDF4PMC, our workflow
1. Metadata & content
Metadata
Content
RDFized
article
Provenance
NXML
2. Semantic content enrichment
Enriched
content
RDFization
Annotation
RDF4PMC and Bio2RDF
Consuming the dataset, a first prototype
3. Navigating the neighborhood
2. Enriched content
 facts-based
reading
1. Retrieval: Metadata
+ Cloud of annotations
Contextual
reading
Graphical
tools
Interactive zone
Search and retrieval based on human gene names: the term is
resolved with GeneWiki, and the associated UniProt accession is
used in the query
Enriched content based on annotations is
displayed in the interactive zone
Graph-based retrieval for the terms “catalase”; only shared
terms with more than 30 associated biological terms are
included in the results.
Consuming the dataset, SPARQL and API
Retrieval
Service
A list of terms and their related topics
SELECT distinct ?pmid
WHERE {
?article a bibo:AcademicArticle ;
bibo:pmid ?pmid .
?annotation a aot:ExactQualifier ;
ao:annotatesResource ?article ;
ao:hasTopic <http://purl.obolibrary.org/obo/CHEBI_60004> .
}
have been semantically annotated with the biological

entity CHEBI:60004. The semantic annotation comes
from the occurrence of the term “mixture” in any
paragraph of the retrieved articles.
e.g., http://biotea.idiginfo.org/api/topics?term=cancer
e.g., http://biotea.idiginfo.org/api/vocabularies?term=cancer
All terms that start with a specific string (for autocompletion)
e.g.,http://biotea.idiginfo.org/api/terms?prefix=canc
All topics related to a vocabulary
e.g., http://biotea.idiginfo.org/api/topics?vocabulary=po
RDF of articles that include a term
e.g., http://biotea.idiginfo.org/api/articles?term=cancer
Count of RDF of articles that include a term
e.g., http://biotea.idiginfo.org/api/articles?term=cancer&count=true
A list of vocabularies and their prefixes
http://biotea.idiginfo.org/vocabularies
RDF of articles that include a vocabulary
Retrieving PubMed identifier for those articles that
http://biotea.idiginfo.org/api/topics
All vocabularies related to a term
Query expressed in natural language
A list of topics and their related vocabularies
All topics related to a term
SPARQL query
http://biotea.idiginfo.org/api/terms
e.g., http://biotea.idiginfo.org/api/articles?vocabulary=po
AGC and CM have been funded by US DoD Grant MOMRP w81xwh-10-2-0181.