[MOBY-guts] biomoby commit
Simon Twigger
simont at pub.open-bio.org
Wed Apr 28 18:45:19 UTC 2004
simont
Wed Apr 28 14:45:19 EDT 2004
Update of /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege
In directory pub.open-bio.org:/tmp/cvs-serv18172
Modified Files:
MobyServiceOntology.owl
Log Message:
updated OWL file in sync with .pprj
moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege MobyServiceOntology.owl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MobyServiceOntology.owl,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MobyServiceOntology.owl 2004/04/19 15:10:16 1.1
+++ /home/repository/moby/moby-live/Docs/OntologyDevelopment/MobyServiceOntologyProtege/MobyServiceOntology.owl 2004/04/28 18:45:19 1.2
@@ -20,291 +20,412 @@
>0.1</owl:versionInfo>
<owl:imports rdf:resource="http://protege.stanford.edu/plugins/owl/protege"/>
</owl:Ontology>
- <owl:Class rdf:ID="text_plain">
+ <owl:Class rdf:ID="predict_secondary_structure">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#predict_structure"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="PubMed_MEDLINE">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#text_formatted"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="text_xml">
<rdfs:subClassOf>
<owl:Class rdf:about="#String"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="predict_secondary_structure">
+ <owl:Class rdf:ID="display">
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >takes input object and returns a visual representation of that object - plot, graph, image, etc.</rdfs:comment>
<rdfs:subClassOf>
- <owl:Class rdf:about="#predict_structure"/>
+ <owl:Class rdf:about="#bioapplicationService"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="multiple_global_alignment">
+ <owl:Class rdf:ID="by_translation">
<rdfs:subClassOf>
- <owl:Class rdf:about="#global_alignment"/>
+ <owl:Class rdf:about="#conversion"/>
</rdfs:subClassOf>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >returns a translation of the input into a different form</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="FASTA">
+ <owl:Class rdf:ID="find_transcription_factor_binding_sites">
<rdfs:subClassOf>
- <owl:Class rdf:about="#text_formatted"/>
+ <owl:Class rdf:about="#find_sequence_features"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="PubMed_MEDLINE">
+ <owl:Class rdf:ID="text_html">
<rdfs:subClassOf>
- <owl:Class rdf:about="#text_formatted"/>
+ <owl:Class rdf:about="#String"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="filtering">
+ <owl:Class rdf:ID="conversion">
+ <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >TODO: Need to explore this more closely, current subclass structure seems limiting
+</owl:versionInfo>
<rdfs:subClassOf>
- <owl:Class rdf:about="#collection_services"/>
+ <owl:Class rdf:about="#bioapplicationService"/>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >takes group of input objects and filters them by a specified criteria, returns a subset of the group</rdfs:comment>
+ >takes input object and converts it to another format or representation</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="text_xml">
+ <owl:Class rdf:ID="deregistration">
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >removal of services from central repository</rdfs:comment>
<rdfs:subClassOf>
- <owl:Class rdf:about="#String"/>
+ <owl:Class rdf:about="#registryTransaction"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="display">
+ <owl:Class rdf:ID="analysis">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >takes input object and returns a visual representation of that object - plot, graph, image, etc.</rdfs:comment>
+ >a service that performs an bioinformatic analysis upon the input object(s). Inputs are biologically meaningful things.</rdfs:comment>
<rdfs:subClassOf>
<owl:Class rdf:about="#bioapplicationService"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="protein_db_search">
+ <owl:Class rdf:ID="database_services">
<rdfs:subClassOf>
- <owl:Class rdf:about="#database_search"/>
+ <owl:Class rdf:about="#object_manipulation"/>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >searches a protein database</rdfs:comment>
+ >operate on databases to add, delete, update data</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="multiple_local_alignment">
+ <owl:Class rdf:ID="literature_db_search">
<rdfs:subClassOf>
- <owl:Class rdf:about="#local_alignment"/>
+ <owl:Class rdf:about="#database_search"/>
</rdfs:subClassOf>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >searches a literature database</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="by_translation">
+ <owl:Class rdf:ID="nucleotide_db_search">
<rdfs:subClassOf>
- <owl:Class rdf:about="#conversion"/>
+ <owl:Class rdf:about="#database_search"/>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >returns a translation of the input into a different form</rdfs:comment>
+ >searches nucleotide database</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="String">
+ <owl:Class rdf:ID="NucleotideSequence">
<rdfs:subClassOf>
- <owl:Class rdf:about="#objectClass"/>
+ <owl:Class rdf:about="#GenericSequence"/>
</rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="term_lookup">
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >A dictionary-type service that provides definitions for supplied terms
+</rdfs:comment>
<rdfs:subClassOf>
- <owl:Restriction>
- <owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean"
- >true</owl:hasValue>
- <owl:onProperty>
- <owl:ObjectProperty rdf:about="#has_string"/>
- </owl:onProperty>
- </owl:Restriction>
+ <owl:Class rdf:about="#retrieval"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="GenericSequence">
+ <owl:Class rdf:ID="updating">
+ <rdfs:subClassOf rdf:resource="#database_services"/>
+ </owl:Class>
+ <owl:Class rdf:ID="align_structure">
<rdfs:subClassOf>
- <owl:Class rdf:about="#VirtualSequence"/>
+ <owl:Class rdf:about="#alignment"/>
</rdfs:subClassOf>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >alignment using tertiary structure comparison, eg. STAMP</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="infrastructureService">
- <owl:disjointWith>
- <owl:Class rdf:about="#bioapplicationService"/>
- </owl:disjointWith>
+ <owl:Class rdf:ID="collection_services">
<rdfs:subClassOf>
- <owl:Class rdf:about="#serviceClass"/>
+ <owl:Class rdf:about="#object_manipulation"/>
</rdfs:subClassOf>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >operate on collections of objects</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="bioapplicationService">
+ <owl:Class rdf:ID="predict_property">
+ <rdfs:subClassOf rdf:resource="#analysis"/>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >takes input and predicts some property of the input object based on specific algorithms</rdfs:comment>
+ </owl:Class>
+ <owl:Class rdf:ID="WU_BLAST_Text">
<rdfs:subClassOf>
- <owl:Class rdf:about="#serviceClass"/>
+ <owl:Class rdf:about="#text_formatted"/>
</rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="b64_encoded_gif">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#text_base64"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="alignment">
+ <rdfs:subClassOf rdf:resource="#analysis"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >All services that do something related to the bioinformatics applications, data, analyses, etc. themselves. As distinct from services that deal with webservice computing infrastructure - service registration, deregisration, etc.</rdfs:comment>
- <owl:disjointWith rdf:resource="#infrastructureService"/>
+ >Service that aligns two objects</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="find_transcription_factor_binding_sites">
+ <owl:Class rdf:ID="splitting">
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >takes object(s) and breaks apart into subobjects</rdfs:comment>
+ <rdfs:subClassOf rdf:resource="#collection_services"/>
+ </owl:Class>
+ <owl:Class rdf:ID="objectClass">
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >root of bioMOBY Object ontology</rdfs:comment>
+ </owl:Class>
+ <owl:Class rdf:ID="format_parsing">
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >service that takes an input and parses it, analyzing the parts of the input document, returning an organized collection of the parts back to the calling application.</rdfs:comment>
<rdfs:subClassOf>
- <owl:Class rdf:about="#find_sequence_features"/>
+ <owl:Class rdf:about="#bioapplicationService"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="embl_flatfile">
+ <owl:Class rdf:ID="NCBI_BLAST_Text">
<rdfs:subClassOf>
<owl:Class rdf:about="#text_formatted"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="text_html">
- <rdfs:subClassOf rdf:resource="#String"/>
- </owl:Class>
- <owl:Class rdf:ID="conversion">
- <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >TODO: Need to explore this more closely, current subclass structure seems limiting
-</owl:versionInfo>
- <rdfs:subClassOf rdf:resource="#bioapplicationService"/>
+ <owl:Class rdf:ID="inserting">
+ <rdfs:subClassOf rdf:resource="#database_services"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >takes input object and converts it to another format or representation</rdfs:comment>
+ >inserts input object into something - database, file</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="find_digestion_sites">
+ <owl:Class rdf:ID="text_base64">
<rdfs:subClassOf>
- <owl:Class rdf:about="#find_sequence_features"/>
+ <owl:Class rdf:about="#String"/>
</rdfs:subClassOf>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >takes input object and performs digestion, returns collection of subobjects - eg. restriction analysis of DNA, digestion of protein by trypsin, etc.</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="align_sequence">
+ <owl:Class rdf:ID="SimpleAnnotatedJPEGImage">
<rdfs:subClassOf>
- <owl:Class rdf:about="#alignment"/>
+ <owl:Class rdf:about="#text_formatted"/>
</rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="DNASequence">
+ <rdfs:subClassOf rdf:resource="#NucleotideSequence"/>
+ </owl:Class>
+ <owl:Class rdf:ID="text_uuencoded">
<rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty>
- <owl:ObjectProperty rdf:about="#has_input"/>
- </owl:onProperty>
- <owl:allValuesFrom rdf:resource="#GenericSequence"/>
- </owl:Restriction>
+ <owl:Class rdf:about="#String"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="RNASequence">
+ <owl:Class rdf:ID="DateTime">
<rdfs:subClassOf>
- <owl:Class rdf:about="#NucleotideSequence"/>
+ <owl:Class rdf:about="#String"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="deregistration">
- <rdfs:subClassOf rdf:resource="#infrastructureService"/>
+ <owl:Class rdf:ID="predict_tertiary_structure">
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >prediction of structural features - eg coils, sheets in protein
+</rdfs:comment>
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#predict_structure"/>
+ </rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="database_services">
+ <owl:Class rdf:ID="resolution">
<rdfs:subClassOf>
- <owl:Class rdf:about="#object_manipulation"/>
+ <owl:Class rdf:about="#infrastructureService"/>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >operate on databases to add, delete, update data</rdfs:comment>
+ >provides a resolution service, eg LSID resolution</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="analysis">
+ <owl:Class rdf:ID="format_validation">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >a service that performs an bioinformatic analysis upon the input object(s). Inputs are biologically meaningful things.</rdfs:comment>
- <rdfs:subClassOf rdf:resource="#bioapplicationService"/>
+ >validates the format of the input, eg SQUIZZ tool</rdfs:comment>
+ <rdfs:subClassOf rdf:resource="#format_parsing"/>
</owl:Class>
- <owl:Class rdf:ID="grouping">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >takes a list of input objects and groups them accoring to criteria, returns a collection of the grouped objects or the same list with group information included.</rdfs:comment>
+ <owl:Class rdf:ID="GFF2">
<rdfs:subClassOf>
- <owl:Class rdf:about="#collection_services"/>
+ <owl:Class rdf:about="#GFF"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="local_alignment">
- <rdfs:subClassOf rdf:resource="#align_sequence"/>
+ <owl:Class rdf:ID="locate_feature">
+ <rdfs:subClassOf rdf:resource="#analysis"/>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >takes input and finds features based on comparisons to known things, eg. restriction site sequence (as opposed to prediction by algorithm)</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="by_summarization">
+ <owl:Class rdf:ID="calculation">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >returns a summarized version of the input</rdfs:comment>
- <rdfs:subClassOf rdf:resource="#conversion"/>
+ >service that calculates something: pI of protein sequence, MWt, Hydrophobicity, etc.</rdfs:comment>
+ <rdfs:subClassOf rdf:resource="#analysis"/>
</owl:Class>
- <owl:Class rdf:ID="pairwise_global_alignment">
+ <owl:Class rdf:ID="GFF2_5">
<rdfs:subClassOf>
- <owl:Class rdf:about="#global_alignment"/>
+ <owl:Class rdf:about="#GFF"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="literature_db_search">
+ <owl:Class rdf:ID="DNASequenceWithGFFFeatures">
+ <rdfs:subClassOf rdf:resource="#DNASequence"/>
+ </owl:Class>
+ <owl:Class rdf:ID="global_alignment">
<rdfs:subClassOf>
- <owl:Class rdf:about="#database_search"/>
+ <owl:Class rdf:about="#align_sequence"/>
</rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="predict_location">
+ <rdfs:subClassOf rdf:resource="#predict_property"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >searches a literature database</rdfs:comment>
+ >predicts the physical location of the input object based on some analysis - eg. protein location within the cell based on signal peptide, transmembrane regions, etc.</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="nucleotide_db_search">
+ <owl:Class rdf:ID="predict_gene_model">
<rdfs:subClassOf>
- <owl:Class rdf:about="#database_search"/>
+ <owl:Class rdf:about="#predict_sequence_feature"/>
</rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="predict_sequence_feature">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >searches nucleotide database</rdfs:comment>
+ >predicts the existence of various features in the input object through the use of a specific algorithm - eg. gene prediction.</rdfs:comment>
+ <rdfs:subClassOf rdf:resource="#predict_property"/>
</owl:Class>
- <owl:Class rdf:ID="NucleotideSequence">
- <rdfs:subClassOf rdf:resource="#GenericSequence"/>
+ <owl:Class rdf:ID="proteinMolecularWeight">
+ <rdfs:subClassOf rdf:resource="#calculation"/>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Calculates a protein's accurate molecular weight</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="text_formatted">
- <rdfs:subClassOf rdf:resource="#text_plain"/>
+ <owl:Class rdf:ID="GFF3">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#GFF"/>
+ </rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="term_lookup">
+ <owl:Class rdf:ID="text_plain">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#String"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="FASTA">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#text_formatted"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="multiple_global_alignment">
+ <rdfs:subClassOf rdf:resource="#global_alignment"/>
+ </owl:Class>
+ <owl:Class rdf:ID="registryTransaction">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >A dictionary-type service that provides definitions for supplied terms
-</rdfs:comment>
+ >services that send data to and from a registry - that perform a registry transaction of some kind.</rdfs:comment>
<rdfs:subClassOf>
- <owl:Class rdf:about="#retrieval"/>
+ <owl:Class rdf:about="#infrastructureService"/>
</rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="updating">
- <rdfs:subClassOf rdf:resource="#database_services"/>
+ <owl:Class rdf:ID="filtering">
+ <rdfs:subClassOf rdf:resource="#collection_services"/>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >takes group of input objects and filters them by a specified criteria, returns a subset of the group</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="align_structure">
+ <owl:Class rdf:ID="protein_db_search">
<rdfs:subClassOf>
- <owl:Class rdf:about="#alignment"/>
+ <owl:Class rdf:about="#database_search"/>
</rdfs:subClassOf>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >alignment using tertiary structure comparison, eg. STAMP</rdfs:comment>
+ >searches a protein database</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="amino_acid_to_nucleotide">
- <rdfs:subClassOf rdf:resource="#by_translation"/>
+ <owl:Class rdf:ID="multiple_local_alignment">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#local_alignment"/>
+ </rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="collection_services">
+ <owl:Class rdf:ID="GenericSequence">
<rdfs:subClassOf>
- <owl:Class rdf:about="#object_manipulation"/>
+ <owl:Class rdf:about="#VirtualSequence"/>
</rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="String">
+ <rdfs:subClassOf rdf:resource="#objectClass"/>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty>
+ <owl:ObjectProperty rdf:about="#has_string"/>
+ </owl:onProperty>
+ <owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean"
+ >true</owl:hasValue>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="infrastructureService">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >operate on collections of objects</rdfs:comment>
+ >service that is related to computing infrastructure, does not operate on biological object(s). Eg. performing webservice registration</rdfs:comment>
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#serviceClass"/>
+ </rdfs:subClassOf>
</owl:Class>
- <owl:Class rdf:ID="database_search">
+ <owl:Class rdf:ID="bioapplicationService">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >searches a database using supplied input objects as search criteria, returns a list of hits</rdfs:comment>
+ >a service that performs a task upon biological or objects</rdfs:comment>
<rdfs:subClassOf>
- <owl:Class rdf:about="#search"/>
+ <owl:Class rdf:about="#serviceClass"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="embl_flatfile">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#text_formatted"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:ID="align_sequence">
+ <rdfs:subClassOf rdf:resource="#alignment"/>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:allValuesFrom rdf:resource="#GenericSequence"/>
+ <owl:onProperty>
+ <owl:ObjectProperty rdf:about="#has_input"/>
+ </owl:onProperty>
+ </owl:Restriction>
</rdfs:subClassOf>
</owl:Class>
+ <owl:Class rdf:ID="find_digestion_sites">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#find_sequence_features"/>
+ </rdfs:subClassOf>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >takes input object and performs digestion, returns collection of subobjects - eg. restriction analysis of DNA, digestion of protein by trypsin, etc.</rdfs:comment>
+ </owl:Class>
+ <owl:Class rdf:ID="RNASequence">
+ <rdfs:subClassOf rdf:resource="#NucleotideSequence"/>
+ </owl:Class>
+ <owl:Class rdf:ID="local_alignment">
+ <rdfs:subClassOf rdf:resource="#align_sequence"/>
+ </owl:Class>
+ <owl:Class rdf:ID="grouping">
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >takes a list of input objects and groups them accoring to criteria, returns a collection of the grouped objects or the same list with group information included.</rdfs:comment>
+ <rdfs:subClassOf rdf:resource="#collection_services"/>
+ </owl:Class>
+ <owl:Class rdf:ID="pairwise_global_alignment">
+ <rdfs:subClassOf rdf:resource="#global_alignment"/>
+ </owl:Class>
+ <owl:Class rdf:ID="by_summarization">
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >returns a summarized version of the input</rdfs:comment>
+ <rdfs:subClassOf rdf:resource="#conversion"/>
+ </owl:Class>
+ <owl:Class rdf:ID="proteinIsoelectricPoint">
+ <rdfs:subClassOf rdf:resource="#calculation"/>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >calculates a protein's isoelectric point</rdfs:comment>
+ </owl:Class>
+ <owl:Class rdf:ID="text_formatted">
+ <rdfs:subClassOf rdf:resource="#text_plain"/>
+ </owl:Class>
+ <owl:Class rdf:ID="amino_acid_to_nucleotide">
+ <rdfs:subClassOf rdf:resource="#by_translation"/>
+ </owl:Class>
<owl:Class rdf:ID="retrieval">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Service thats main function is to take an input and retrieves information related to the input, eg. using a term to retrieve a definition, a genbank accession to get a flat file.</rdfs:comment>
<rdfs:subClassOf rdf:resource="#bioapplicationService"/>
</owl:Class>
- <owl:Class rdf:ID="predict_property">
- <rdfs:subClassOf rdf:resource="#analysis"/>
+ <owl:Class rdf:ID="database_search">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >takes input and predicts some property of the input object based on specific algorithms</rdfs:comment>
+ >searches a database using supplied input objects as search criteria, returns a list of hits</rdfs:comment>
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#search"/>
+ </rdfs:subClassOf>
</owl:Class>
<owl:Class rdf:ID="predict_structure">
<rdfs:subClassOf rdf:resource="#predict_property"/>
</owl:Class>
<owl:Class rdf:ID="nucleotide_to_amino_acid">
- <rdfs:subClassOf rdf:resource="#by_translation"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>translates a nucleic acid sequence to a protein sequence</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:ID="WU_BLAST_Text">
- <rdfs:subClassOf rdf:resource="#text_formatted"/>
+ <rdfs:subClassOf rdf:resource="#by_translation"/>
</owl:Class>
<owl:Class rdf:ID="b64_encoded_jpeg">
- <rdfs:subClassOf>
- <owl:Class rdf:about="#text_base64"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:ID="b64_encoded_gif">
- <rdfs:subClassOf>
- <owl:Class rdf:about="#text_base64"/>
- </rdfs:subClassOf>
+ <rdfs:subClassOf rdf:resource="#text_base64"/>
</owl:Class>
<owl:Class rdf:ID="serviceClass">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Root of the bioMOBY service ontology</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="alignment">
- <rdfs:subClassOf rdf:resource="#analysis"/>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Service that aligns two objects</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:ID="service_registration">
- <rdfs:subClassOf>
- <owl:Class rdf:about="#registration"/>
- </rdfs:subClassOf>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >registers services with central repository, eg. MOBY Central</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:ID="splitting">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >takes object(s) and breaks apart into subobjects</rdfs:comment>
- <rdfs:subClassOf rdf:resource="#collection_services"/>
+ <owl:Class rdf:ID="IntAct_XML">
+ <rdfs:subClassOf rdf:resource="#text_xml"/>
</owl:Class>
<owl:Class rdf:ID="find_sequence_features">
<rdfs:subClassOf>
@@ -313,43 +434,26 @@
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>service searches sequence data for known patterns</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="IntAct_XML">
- <rdfs:subClassOf rdf:resource="#text_xml"/>
- </owl:Class>
<owl:Class rdf:ID="VirtualSequence">
- <rdfs:subClassOf>
- <owl:Class rdf:about="#objectClass"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:ID="objectClass">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >root of bioMOBY Object ontology</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:ID="format_parsing">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >service that takes an input and parses it, analyzing the parts of the input document, returning an organized collection of the parts back to the calling application.</rdfs:comment>
- <rdfs:subClassOf rdf:resource="#bioapplicationService"/>
+ <rdfs:subClassOf rdf:resource="#objectClass"/>
</owl:Class>
<owl:Class rdf:ID="object_manipulation">
<rdfs:subClassOf rdf:resource="#bioapplicationService"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>manipulation services - take input objects and manipulate them in some way</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="NCBI_BLAST_Text">
- <rdfs:subClassOf rdf:resource="#text_formatted"/>
+ <owl:Class rdf:ID="by_pattern_matching">
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >searches for the occurance of known pattern(s) - eg. transcription factor binding sites</rdfs:comment>
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Not sure if the method should be defined by the ontology at this level</rdfs:comment>
+ <rdfs:subClassOf rdf:resource="#locate_feature"/>
</owl:Class>
<owl:Class rdf:ID="clustering">
<rdfs:subClassOf rdf:resource="#analysis"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>performs some type of cluster analysis on input data</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="by_pattern_matching">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >searches for the occurance of known pattern(s) - eg. transcription factor binding sites</rdfs:comment>
- <rdfs:subClassOf>
- <owl:Class rdf:about="#locate_feature"/>
- </rdfs:subClassOf>
- </owl:Class>
<owl:Class rdf:ID="Genbank_flatfile">
<rdfs:subClassOf rdf:resource="#text_formatted"/>
</owl:Class>
@@ -359,46 +463,25 @@
<rdfs:subClassOf rdf:resource="#term_lookup"/>
</owl:Class>
<owl:Class rdf:ID="find_repeats">
- <rdfs:subClassOf rdf:resource="#by_pattern_matching"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>repeat finding in sequence data</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:ID="inserting">
- <rdfs:subClassOf rdf:resource="#database_services"/>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >inserts input object into something - database, file</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:ID="text_base64">
- <rdfs:subClassOf rdf:resource="#String"/>
+ <rdfs:subClassOf rdf:resource="#find_sequence_features"/>
</owl:Class>
<owl:Class rdf:ID="GFF">
<rdfs:subClassOf rdf:resource="#text_formatted"/>
</owl:Class>
- <owl:Class rdf:ID="SimpleAnnotatedJPEGImage">
- <rdfs:subClassOf rdf:resource="#text_formatted"/>
- </owl:Class>
<owl:Class rdf:ID="hapmap_text">
<rdfs:subClassOf rdf:resource="#text_formatted"/>
</owl:Class>
- <owl:Class rdf:ID="DNASequence">
- <rdfs:subClassOf rdf:resource="#NucleotideSequence"/>
- </owl:Class>
- <owl:Class rdf:ID="text_uuencoded">
- <rdfs:subClassOf rdf:resource="#String"/>
- </owl:Class>
<owl:Class rdf:ID="dictionary_lookup">
<rdfs:subClassOf rdf:resource="#term_lookup"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>returns the definition of a keyword as defined in a particular dictionary of terms.</rdfs:comment>
</owl:Class>
- <owl:Class rdf:ID="DateTime">
- <rdfs:subClassOf rdf:resource="#String"/>
- </owl:Class>
- <owl:Class rdf:ID="predict_tertiary_structure">
+ <owl:Class rdf:ID="dnaMeltingTemperature">
+ <rdfs:subClassOf rdf:resource="#calculation"/>
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >prediction of structural features - eg coils, sheets in protein
-</rdfs:comment>
- <rdfs:subClassOf rdf:resource="#predict_structure"/>
+ >Calculates the melting point of a given DNA sequence</rdfs:comment>
</owl:Class>
<owl:Class rdf:ID="search">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
@@ -408,33 +491,16 @@
<owl:Class rdf:ID="pairwise_local_alignment">
<rdfs:subClassOf rdf:resource="#local_alignment"/>
</owl:Class>
- <owl:Class rdf:ID="resolution">
- <rdfs:subClassOf rdf:resource="#bioapplicationService"/>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >provides a resolution service, eg LSID resolution</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:ID="GFF2">
- <rdfs:subClassOf rdf:resource="#GFF"/>
- </owl:Class>
- <owl:Class rdf:ID="format_validation">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >validates the format of the input, eg SQUIZZ tool</rdfs:comment>
- <rdfs:subClassOf rdf:resource="#format_parsing"/>
- </owl:Class>
<owl:Class rdf:ID="deleting">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>service deletes data from a database</rdfs:comment>
<rdfs:subClassOf rdf:resource="#database_services"/>
</owl:Class>
- <owl:Class rdf:ID="locate_feature">
- <rdfs:subClassOf rdf:resource="#analysis"/>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >takes input and finds features based on comparisons to known things, eg. restriction site sequence (as opposed to prediction by algorithm)</rdfs:comment>
- </owl:Class>
<owl:Class rdf:ID="GFF1">
<rdfs:subClassOf rdf:resource="#GFF"/>
</owl:Class>
<owl:Class rdf:ID="Integer">
+ <rdfs:subClassOf rdf:resource="#objectClass"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:hasValue rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean"
@@ -444,31 +510,11 @@
</owl:onProperty>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf rdf:resource="#objectClass"/>
- </owl:Class>
- <owl:Class rdf:ID="calculation">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >service that calculates something: pI of protein sequence, MWt, Hydrophobicity, etc.</rdfs:comment>
- <rdfs:subClassOf rdf:resource="#analysis"/>
</owl:Class>
<owl:Class rdf:ID="registration">
<rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>Allows registration of objects (and/or services) in specified repositories.</rdfs:comment>
- <rdfs:subClassOf rdf:resource="#infrastructureService"/>
- </owl:Class>
- <owl:Class rdf:ID="DNASequenceWithGFFFeatures">
- <rdfs:subClassOf rdf:resource="#DNASequence"/>
- </owl:Class>
- <owl:Class rdf:ID="GFF2_5">
- <rdfs:subClassOf rdf:resource="#GFF"/>
- </owl:Class>
- <owl:Class rdf:ID="global_alignment">
- <rdfs:subClassOf rdf:resource="#align_sequence"/>
- </owl:Class>
- <owl:Class rdf:ID="predict_location">
- <rdfs:subClassOf rdf:resource="#predict_property"/>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >predicts the physical location of the input object based on some analysis - eg. protein location within the cell based on signal peptide, transmembrane regions, etc.</rdfs:comment>
+ <rdfs:subClassOf rdf:resource="#registryTransaction"/>
</owl:Class>
<owl:Class rdf:ID="merging">
<rdfs:subClassOf rdf:resource="#collection_services"/>
@@ -490,24 +536,16 @@
<owl:Class rdf:ID="AminoAcidSequence">
<rdfs:subClassOf rdf:resource="#GenericSequence"/>
</owl:Class>
- <owl:Class rdf:ID="predict_gene_model">
- <rdfs:subClassOf>
- <owl:Class rdf:about="#predict_sequence_feature"/>
- </rdfs:subClassOf>
- </owl:Class>
<owl:Class rdf:ID="NCBI_Blast_XML">
<rdfs:subClassOf rdf:resource="#text_xml"/>
</owl:Class>
- <owl:Class rdf:ID="predict_sequence_feature">
- <rdfs:subClassOf rdf:resource="#predict_property"/>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >predicts the existence of various features in the input object through the use of a specific algorithm - eg. gene prediction.</rdfs:comment>
- </owl:Class>
<owl:Class rdf:ID="Tree">
<rdfs:subClassOf rdf:resource="#text_formatted"/>
</owl:Class>
- <owl:Class rdf:ID="GFF3">
- <rdfs:subClassOf rdf:resource="#GFF"/>
+ <owl:Class rdf:ID="predictHydropathy">
+ <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Predicts the hydrophilic/hydrophobic proile of a sequence</rdfs:comment>
+ <rdfs:subClassOf rdf:resource="#predict_structure"/>
</owl:Class>
<owl:ObjectProperty rdf:ID="has_name">
<rdfs:subPropertyOf>
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