HCLSIG BioRDF Subgroup/Data

X Note: This page needs to be updated, some old content should probably be transferred to other pages

Data generated in HCLS IG second charter

/DBpedia_extracted_data Data extracted from DBpedia

Data Sources in RDF/OWL (overview of some datasets, last updated in 2007)

||  Ontology / Dataset || Ontology type || Content ||
||  Annotea Bookmark File || RDF / Instance style || bibliographic information ||
||  Antibodies || ? || ||
||  BAMS || OWL DL / Class style || Neuroanatomy, neuron classification and description ||
||  BIND in BioPAX || OWL DL / Instance style || Molecular interactions ||
||  Biocyc, Reactome, KEGG || ? || Molecular interactions, bibliographic information ||
||  Biocyc, Reactome, KEGG, INOH in BioPAX || OWL DL / Instance style || Molecular interactions, bibliographic information ||
||  Reactome in bio-zen || OWL DL / Instance style || Molecular interactions, bibliographic information ||
||  Entrez Gene || OWL DL || sequence information, bibliographic information ||
||  /Enzymes (a subset) || RDF / Instance style || ||
||  GO (a subset) || RDF / Instance style || ||
||  HIVSDB || || ||
||  /IntAct (a subset) || RDF / Instance style || Molecular interactions ||
||  /KEGG (a subset) || RDF / Instance style || ||
||  MeSH || RDF / Instance style || subject headings ||
||  MGED || OWL DL  || terminology (mircoarrays) ||
||  Neurocommons data (not yet officially released) || OWL DL / Instance style || molecular interactions, bibliographic information||
||  /OMIM (a subset) || RDF / Instance style || ||
||  PDSP Ki(at bottom of page) || OWL DL / Instance style|| Molecular interactions, bibliographic information ||
||  /Pubmed (a subset) || RDF / Instance style || bibliographic information ||
||  SwissProt Keywords (a subset) || ||
||  SenseLab (RDF version) || RDF / Instance style || Neuroanatomy, Neuron classification and description, bibliographic information, hypotheses ||
||  SenseLab (OWL version) || OWL DL / Class style || Neuroanatomy, Neuron classification and description, bibliographic information, hypotheses ||
||  SMID || ? || ||
||  SWAN publication and hypothesis data (new OWL version) || OWL DL / Instance style || hypotheses, bibliographic information||
||  /Taxonomy (a subset) || || ||
||  UniProt || RDF / Instance style || sequence information ||

The following ontologies from the OBO repository are not listed in the table, but are of potential importance: MeSH (note that current OBO version has flaws), GO, Chebi, Celltype, Entrez Taxonomy. They can be downloaded as 'RDF / Instance style' or 'OWL / Class style' from http://www.berkeleybop.org/ontologies/

Mappings

||  Ontology / Dataset || Ontology type || Content ||
||  Senselab / OBI / Birnlex / BAMS / BFO mapping (under construction) || OWL / Class style || ||
||  /Enzymes 2 KEGG (a subset) || RDF / Instance style || ||
||  GO 2 Enzymes (a subset) || RDF / Instance style || ||
||  /GO 2 Keywords (a subset) || RDF / Instance style || ||
||  /GO 2 OMIM (a subset) || RDF / Instance style || ||
||  /GO 2 Probe (a subset) || RDF / Instance style  ||  ||
||  GO 2 Protein (a subset) || RDF / Instance style || ||
||  GO 2 PubMed (a subset) || RDF / Instance style || ||
||  /Keyword 2 Protein (a subset) || RDF / Instance style || ||
||  /Protein 2 IntAct (a subset) || RDF / Instance style || ||

Mappings and their benefits should be described on the Mappings of neuroscience ontologies and their advantages wiki page.

Description of these tables

Ontology types: Describes whether the ontology is pure RDF (without or mostly without OWL constructs), OWL DL (including ontologies that are actually OWL lite and ontologies that are supposed to be OWL DL but classify as OWL Full because of some errors in ontology design) or OWL Full (ontologies that are intended to be OWL Full). Furthermore, we distinguish between 'Class style' (ontologies that mostly rely on classes and property restrictions for the expression of data and information) and 'Instance style' (ontologies that have a smaller set of classes that act as a 'schema', but mostly rely on instances for the expression of data and information).

Table of datasource in the HCLS KB (last updated in 2007)

Table of datasets relevant to the HCLS/Neurocommons DB, drafted during the Face-to-Face meeting in Boston 2007-04-11

NeuronDB

• protein (channels/receptors)
• neurotransmitters
• neuroanatomy
• cell
• compartments
• currents

BAMS

• protein -> NeuronDB.protein
• neuroanatomy
• cells
• metabolites -> NeuronDB.channels
• pubmed ID

NC Annotations

 {links genes (and some processes) to pubmed (articles?)}
 {human (by interpretation)}

• genes or gene products (proteins)
• processes
• cells (maybe)
• pubmed papers

Allen Brain Atlas (mouse)

• genes
• brain images
• gross anatomy -> neuroanatomy -> neuroanatomy

Homologene

• genes {pairs}
• species {pairs}
• orthologies
• proofs

SWAN

• pubmed ID
• hypothesis statements (discourse ontology)
• research questions (discourse ontology)
• evidence
• genes

Entrez Gene (human/mouse/rat)

• gene
• protein
• GO terms

 {this protien catalyzes alcohol to alkalide}

• pubmed ID
• interaction (genes/protien)
• chromosome
• chromosome location

GO (human/mouse/rat)

• molecular function
• cell component
• biological process
• annotation gene (tbd)
• pubmed ID

Mammalian Phenotype (human/mouse/rat)

• genes
• phenotypes
• disease
• pubmed ID (J#)

PDSPki (biopax)

• proteins (receptors)
• chemicals
• neurotransmitter

BrainPharm (vertebrates) {pathological processes}

• drug
• drug effect
• pathological agent
• pathological effect
• receptors
• channels
• cell type
• pubmed ID
• disease

AlzGene

• gene
• polymorphism
• population
• associated Alz diagnosis

Antibodies

• genes
• antibodies

PubChem

• compound name
• compound structure
• compound properties
• (mesh terms)

MESH

• drugs
• anatomy
• phenotypes
• compounds
• chemicals
• pubmed ID
• pubchem

Reactome (human+) (biopax)

• genes/proteins
• interactions
• cellular location (component)
• processes (GO links)