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Núria Queralt Rosinach edited this page May 9, 2014 · 38 revisions

Lead Resource

NCBO BioPortal is a repository of over 350 biomedical ontologies, and provides services to annotate text with ontology terms, and ontology-based data exploration

Participant Resources

Bio2RDF is an open-source project that uses Semantic Web technologies to build and provide the largest network of Linked Data for the Life Sciences. Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked Data from a diverse set of heterogeneously formatted sources obtained from multiple data providers.

BridgeDb provides a framework for identifier mapping and annotation for genes, proteins, metabolites and drugs. The project includes default databases that cover dozens of species and over hundred major identifier and annotation datasources. BridgeDb is also hosted as a web service for REST queries.

CRAFT The Colorado Richly Annotated Full-Text (CRAFT) Corpus is a collection of 97 (67 currently publicly available) full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically. CRAFT identifies all (nearly) mentions (approx. 100,000 in the 67 articles) of (nearly) all concepts from eight prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, and the three subontologies of the Gene Ontology.

DGIdb is a drug-gene database integrating associations from several public and expert-curated data sources. DGIdb can be queried through a [web interface] (http://dgidb.genome.wustl.edu/) and an API (http://dgidb.genome.wustl.edu/api).

  • contact: @The Genome Institute at Washington University
    • Malachi Griffith, Obi Griffith

DisGeNET is a gene-disease database integrating gene-disease associations from several public, expert, curated data sources and text mining derived associations. DisGeNET can be queried through a [web interface] (http://ibi.imim.es/web/DisGeNET/v01/search), by a plugin created for Cytoscape, by a faceted browser or a SPARQL endpoint

  • Tutorial material
  • contact:
    • browser and plugin: Janet Piñero
    • Linked Data: Núria Queralt Rosinach

dkNET is a SciCrunch community portal that aims to provide seamless access to large pools of data relevant to the mission of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

ENCODE a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.

  • contact:
    • Venkat Malladi

Knowledge Explorer (KE) / IO Informatics provides a "KE Personal" tool for user interactive, data-driven, ontology / terminology aligned RDF creation, visualization and query. Visual tool generates editable SPARQL directly from networks. Connects directly to NCBO BioPortal(current - April 2014 API) and LOD resources (inc. Open PHACTS, Bio2RDF, ...) via API and / or SPARQL endpoints. Apply for iterative data modeling in interaction Subject Matter Experts. Automate transformation of csv, tsv, xml, xls, (...) resources to well-formed RDF. :ublish mappers, scripts, rules to pipelines (Knime, PLP) for scale-up via command line processing. KE "Pro" version supports direct publication to semantic databases, inference, scale-up (Franz AllegroGraph, Oracle Spatial, OpenLink Virtuoso, [Cray Urika currently in QA]).

Monarch provides tools that will use semantics and statistical models to support navigating through multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in the context of genetic and genomic data.

  • contact: Chris Mungall

MyGene.info is a cloud-based solution to abstract the task of building a gene annotation database into a set of scalable and extensible web services. End users have access to two simple-to-use REST web services for gene annotation query and retrieval, without worrying about designing, building and maintaining a dedicated database. The current system is being extended to allow user contributions and the same concept can be applied to other biological annotations (e.g. variants).

NDEx open-source REST server platform enabling sharing, storing, accessing, and publishing biological networks in multiple formats. Public website based on the NDEx platform in beta. Mission to enable applications based on the NDEx server platform.

  • contact:
    • Dexter Pratt

Neuroscience Information Framework is a dynamic data discovery index of more than 200 federated resources with an associated semantic framework. NIF provides data services for search and exploration and terminology services to annotate text.

Open PHACTS is a Europe based IMI project that developed a semantic web based resource that combines resources like CHEMBL, UniProt, DisGeNET and WikiPathways and allowed mapping between these using a BridgeDb based identifier mapping system (extended to work with URI's, closely working with identifiers.org), a ConceptWiki based identity resolution service and a chemistry resolution service. Open PHACTS can be queried through an API that submits predeveloped complex SPARQL queries. WikiPathways is a community-curated database of biological pathways. Pathway information is captured as human readable diagrams which are drawn and annotated with standard database identifiers, ontology terms and pubmed references. The data is available as XML and SVG, via REST web services, and, of course, as RDF and Linked Data.

Reactome is a manually curated open-source open-data resource of human pathways and reactions. The data model has been extended to support annotation of disease processes due to infectious agents and to mutation. Reactome data is available as XML, BioPAX, SBML, SBGN, MySQL dump, flat files, via REST web services.

SciCrunch is a cooperative data platform which provides access to more than 200 federated resources and provides communities the ability to configure customized search and discovery portals.

WikiPathways is a community-curated database of biological pathways. Pathway information is captured as human readable diagrams which are drawn and annotated with standard database identifiers, ontology terms and pubmed references. The data is available as XML and SVG, via REST web services, and, of course, as RDF and Linked Data.

Rhizi A online collaborative document for inputting and exploring graphs

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