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dto_vocabulary_pfam_domain.owl
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dto_vocabulary_pfam_domain.owl
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<?xml version="1.0"?>
<!DOCTYPE rdf:RDF [
<!ENTITY DTO "http://dto.org/DTO/" >
<!ENTITY foaf "http://xmlns.com/foaf/0.1/" >
<!ENTITY life "http://www.lifekb.org/life#" >
<!ENTITY owl "http://www.w3.org/2002/07/owl#" >
<!ENTITY obo "http://purl.obolibrary.org/obo/" >
<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
<!ENTITY bto "http://purl.obolibrary.org/obo/bto#" >
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
<!ENTITY dto "http://www.drugtargetontology.org/dto/" >
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
<!ENTITY core "http://purl.obolibrary.org/obo/uberon/core#" >
<!ENTITY dc "http://purl.org/dc/elements/1.1/" >
<!ENTITY oboInOwl "http://www.geneontology.org/formats/oboInOwl#">]>
<rdf:RDF xmlns="http://www.drugtargetontology.org/dto/dto_vocabulary_pfam_domain.owl#"
xml:base="http://www.drugtargetontology.org/dto/dto_vocabulary_pfam_domain.owl"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:life="http://www.lifekb.org/life#"
xmlns:core="&obo;uberon/core#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bto="&obo;bto#"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:dto="http://www.drugtargetontology.org/dto/"
xmlns:DTO="http://dto.org/DTO/"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:dc="http://purl.org/dc/elements/1.1/">
<owl:Ontology rdf:about="http://www.drugtargetontology.org/dto/dto_vocabulary_pfam_domain.owl">
<owl:versionIRI rdf:resource="http://www.drugtargetontology.org/dto/dto_vocabulary_pfam_domain.owl"/>
<rdfs:label>Drug Target Ontology</rdfs:label>
<rdfs:label>DTO</rdfs:label>
<owl:versionInfo>1.0</owl:versionInfo>
<dc:date>2 Nov 2017</dc:date>
<dc:contributor>Yu Lin, Saurabh Mehta, Hande Küçük- McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L. Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J. Yang, Cristian G. Bologa, Tudor Oprea*, Stephan C. Schürer*</dc:contributor>
<rdfs:comment xml:lang="en">contact: Stephan Schurer: stephan dot schurer at gmail dot com</rdfs:comment>
<dc:description>
Drug target ontology files Drug Target Ontology (DTO) is being developed at the University of Miami in the research group of Stephan Schürer.
DTO is supported by grant U54CA189205 (Illuminating the Druggable Genome Knowledge Management Center, Tudor Oprea, PI) awarded by the NCI through
the NIH Common Fund. It is a component of the Illuminating the Druggable Genome (IDG) project (https://commonfund.nih.gov/idg). The DTO project
develops a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families. The DTO is developed
as a reference for drug targets with the longer-term goal to create a community standard that will facilitate the integration of diverse drug discovery
information from numerous heterogeneous resources. The first version of the DTO consists of asserted class hierarchies of the four IDG protein families,
GPCRs, kinases, ion channels, and nuclear hormone receptors. Protein classes are linked to tissue and disease via different levels of confidence. DTO
also contains drug target development classifications, a large collection of cell lines from the LINCS project and relevant cell-disease and cell-tissue
relations. DTO is modeled in OWL2-DL to enable further classification by inference reasoning and SPARQL queries. DTO is implemented following a
modularization approach. DTO will serve as the organizational framework for drug targets in the IDG PHAROS User Interface Portal (https://pharos.nih.gov).
</dc:description>
<dc:license rdf:resource="https://creativecommons.org/licenses/by-sa/4.0/"/>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://www.drugtargetontology.org/dto/DTO_63000000 -->
<owl:Class rdf:about="http://www.drugtargetontology.org/dto/DTO_63000000">
<rdfs:label rdf:datatype="&xsd;string">pfam domain</rdfs:label>
<obo:IAO_0000115>The kinase domain information from the pfam database.</obo:IAO_0000115>
<obo:IAO_0000115>Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models</obo:IAO_0000115>
</owl:Class>
<!-- http://www.drugtargetontology.org/dto/DTO_63000002 -->
<owl:Class rdf:about="http://www.drugtargetontology.org/dto/DTO_63000002">
<rdfs:label rdf:datatype="&xsd;string">ABC1</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.drugtargetontology.org/dto/DTO_63000000"/>
<obo:IAO_0000115>A Pfam protein family that includes ABC1 from yeast and AarF from E. coli . These proteins have a nuclear or mitochondrial subcellular location in eukaryotes. The exact molecular functions of these proteins is not clear, however yeast ABC1 suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex [1] and E. coli AarF is required for ubiquinone production. It has been suggested that members of the ABC1 family are novel chaperonins. These proteins are unrelated to the ABC transporter proteins.</obo:IAO_0000115>
<obo:IAO_0000119>http://pfam.xfam.org/family/ABC1</obo:IAO_0000119>
<obo:IAO_0000119>http://pfam.xfam.org/family/PF01504</obo:IAO_0000119>
</owl:Class>
<!-- http://www.drugtargetontology.org/dto/DTO_63000003 -->
<owl:Class rdf:about="http://www.drugtargetontology.org/dto/DTO_63000003">
<rdfs:label rdf:datatype="&xsd;string">Alpha_kinase</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.drugtargetontology.org/dto/DTO_63000000"/>
<obo:IAO_0000115>A Pfam protein family that is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional kinases. The family contains myosin heavy chain kinases and Elongation Factor-2 kinase and a bifunctional ion channel. This family is known as the alpha-kinase family. The structure of the kinase domain revealed unexpected similarity to eukaryotic protein kinases in the catalytic core as well as to metabolic enzymes with ATP-grasp domains.</obo:IAO_0000115>
<obo:IAO_0000119>http://pfam.xfam.org/family/Alpha_kinase</obo:IAO_0000119>
</owl:Class>
<!-- http://www.drugtargetontology.org/dto/DTO_63000004 -->
<owl:Class rdf:about="http://www.drugtargetontology.org/dto/DTO_63000004">
<rdfs:label rdf:datatype="&xsd;string">PI3_PI4_kinase</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.drugtargetontology.org/dto/DTO_63000000"/>
<obo:IAO_0000115>A Pfam protein family that is a family of related intracellular signal transducer enzymes capable of phosphorylating the 3 position hydroxyl group of the inositol ring of phosphatidylinositol (PtdIns).The pathway, with oncogene PIK3CA and tumor suppressor PTEN, is implicated in insensitivity of cancer tumors to insulin and IGF1, and in calorie restriction.</obo:IAO_0000115>
<obo:IAO_0000119>http://pfam.xfam.org/family/PI3_PI4_kinase</obo:IAO_0000119>
</owl:Class>
<!-- http://www.drugtargetontology.org/dto/DTO_63000005 -->
<owl:Class rdf:about="http://www.drugtargetontology.org/dto/DTO_63000005">
<rdfs:label rdf:datatype="&xsd;string">PIP5K</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.drugtargetontology.org/dto/DTO_63000000"/>
<obo:IAO_0000115>A Pfam protein family that contains a region from the common kinase core found in the type I phosphatidylinositol-4-phosphate 5-kinase (PIP5K) family as described in [1]. The family consists of various type I, II and III PIP5K enzymes. PIP5K catalyses the formation of phosphoinositol-4,5-bisphosphate via the phosphorylation of phosphatidylinositol-4-phosphate a precursor in the phosphinositide signaling pathway.</obo:IAO_0000115>
</owl:Class>
<!-- http://www.drugtargetontology.org/dto/DTO_63000006 -->
<owl:Class rdf:about="http://www.drugtargetontology.org/dto/DTO_63000006">
<rdfs:label rdf:datatype="&xsd;string">Pkinase</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.drugtargetontology.org/dto/DTO_63000000"/>
<obo:IAO_0000115>A Pfam protein family that is a structurally conserved protein domain containing the catalytic function of protein kinases. Protein kinases are a group of enzymes that move a phosphate group onto proteins, in a process called phosphorylation. This functions as an on/off switch for many cellular processes, including metabolism, transcription, cell cycle progression, cytoskeletal rearrangement and cell movement, apoptosis, and differentiation. They also function in embryonic development, physiological responses, and in the nervous and immune system. Abnormal phosphorylation causes many human diseases, including cancer, and drugs that affect phosphorylation can treat those diseases.</obo:IAO_0000115>
<obo:IAO_0000119>http://pfam.xfam.org/family/PF00069</obo:IAO_0000119>
</owl:Class>
<!-- http://www.drugtargetontology.org/dto/DTO_63000007 -->
<owl:Class rdf:about="http://www.drugtargetontology.org/dto/DTO_63000007">
<rdfs:label rdf:datatype="&xsd;string">Pkinase_Tyr</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.drugtargetontology.org/dto/DTO_63000006"/>
<obo:IAO_0000115>A Pfam protein family that attaches phosphate groups to other amino acids (serine and threonine). Phosphorylation of proteins by kinases is an important mechanism in communicating signals within a cell (signal transduction) and regulating cellular activity, such as cell division.Tyrosine kinases are a subclass of protein kinase.</obo:IAO_0000115>
<obo:IAO_0000119>http://pfam.xfam.org/family/Pkinase_Tyr
</obo:IAO_0000119>
</owl:Class>
<!-- http://www.drugtargetontology.org/dto/DTO_63000008 -->
<owl:Class rdf:about="http://www.drugtargetontology.org/dto/DTO_63000008">
<rdfs:label rdf:datatype="&xsd;string">RIO1</rdfs:label>
<rdfs:subClassOf rdf:resource="http://www.drugtargetontology.org/dto/DTO_63000000"/>
<obo:IAO_0000115>A Pfam protein family that is of atypical serine kinases which are found in archaea, bacteria and eukaryotes. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome </obo:IAO_0000115>
<obo:IAO_0000119>http://pfam.xfam.org/family/RIO1</obo:IAO_0000119>
</owl:Class>
</rdf:RDF>