Investigation

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Investigation


Investigations/Studies/Assays/Data are modeled according to ISA-TAB standards.

Investigation: High level concept to link related studies.

Study: The central ISA-TAB unit containing information on the subjet under study, its characteristics and any treatments applied.

Assay: Tests performed either on material taken from the subject or on the whole initial subject, which produce qualitative or quantitative measurements (data).

Data: OpenTox Datasets or external files in native or other formats.

Investigations can be queried with SPARQL. REST operations are avialble for accessing individual investigations, studies, assays and data.

Investigations are created by submitting a zip archive with ISA-TAB files. Individual studies, assays and datafiles can be submitted as ISA-TAB files (studies, assays) or as native data files (e.g. Affymetrix CEL files).

Uploading ISA-TAB archives: Investigations can be uploaded in a zip archive with all ISA-TAB files in a single folder.

Uploading individual ISA-TAB files: It is possible to upload individual data and study/assay ISA-TAB files. In this case the client has to ensure that ISA-TAB references are valid URIs or relative paths.

Filenames: ISA-TAB filenames (in zip archives and individual files) have to follow the conventions:

i_*.txt: Investigation
s_*.txt: Study
a_*.txt: Assay
all other filenames will be interpreted as data files

Filenames have to be unique within an investigation. Submissions with conflicting filenames will not be accepted and return a 400 (Bad Request) error. Existing files in an investigation can be queried with GET /investigation/{id}; Accept: text/uri-list.

Contents

Investigation

An Investigation is a collection of related studies.

A Study has associated Assays, it is the result of executing a set of Protocols. A Study has an Author (an User).

An Assay serves as a container, associating a Protocol with the generated data

Data can be either an OpenTox dataset or a native data file (e.g. Affymetrix CEL file).

Get a list of investigations

Description Get a list of all investigations
Resource Investigation
Method GET
URI /investigation
Parameters
Header Parameters Accept:text/uri-list, application/rdf+xml subjectid:SECURITY-TOKEN
Media Type (input)
Results List of investigations
Media Type (output) text/uri-list, application/rdf+xml
Status code 200, 400


Description Get a list of user related investigations
Resource Investigation
Method GET
URI /investigation
Parameters
Header Parameters User:USER_URI subjectid:SECURITY-TOKEN
Media Type (input) Accept:application/rdf+xml, application/json, text/uri-list
Results list of investigations owned/uploaded by a specific user
Media Type (output) application/rdf+xml, application/json, text/uri-list
Status code 200, 400

Links: Page, Edit with form



cURL example

get a URI list of all investigation:

curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation

get a RDF representation of a users investigations:

curl -X GET -k -H 'Accept:application/rdf+xml' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation

get JSON URI/modified date list:

curl -X GET -k -H 'Accept:application/json' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation

get URI list of the users investigations URIs:

curl -X GET -k -H 'Accept:text/uri-list' -H 'user:USER_URI'-H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation

Get a list of uploaded FTP files

Description Get a list of uploaded FTP files of a user
Resource Investigation
Method GET
URI /investigation/ftpfiles
Parameters
Header Parameters Accept: one of < text/uri-list, application/json > , subjectid:SECURITY-TOKEN
Media Type (input)
Results list of files
Media Type (output) application/json text/uri-list
Status code 200, 400

cURL example

curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" https://services.toxbank.net/investigation/ftpfiles

Links: Page, Edit with form



Get informations from published investigations

Description Get information from investigations
Resource Investigation
Method GET
URI investigation/sparql/{template_name}
Parameters params per template(template_name):* no params needed for investigation_and_characteristics, investigations_and_factors and investigations_and_protocols* factorValues: URI array for investigation_by_factors and protocols_by_factors template * geneIdentifiers: Array of Strings for biosearch (e.G.: entrez:3075,genesymbol:HSPD1).
Header Parameters Accept: application/json, subjectid:SECURITY-TOKEN
Media Type (input)
Results Investigation data as json
Media Type (output) application/json
Status code 200, 400, 401, 404

Get information from published investigations via predefined SPARQL queries. (e.G.: https://services.toxbank.net/investigation/sparql/investigations_and_protocols ) . You may also use camelcase notation for templatenames (e.G.: InvestigationsAndProtocols, InvestigationByFactors).

cURL example

curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/sparql/genelist
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" https://services.toxbank.net/investigation/sparql/investigation_and_characteristics
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=http://purl.obolibrary.org/obo/NEWT_4932" https://services.toxbank.net/investigation/sparql/investigation_by_characteristic
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=organism" https://services.toxbank.net/investigation/sparql/investigation_by_characteristic_name
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "value=Saccharomyces cerevisiae (Baker's yeast)" https://services.toxbank.net/investigation/sparql/investigation_by_characteristic_value
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "values=http://purl.obolibrary.org/chebi/CHEBI:39867" https://services.toxbank.net/investigation/sparql/investigation_by_factor
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "factorValues=['http://purl.obolibrary.org/chebi/CHEBI:39867']" https://services.toxbank.net/investigation/sparql/investigation_by_factors
curl -X GET -k -H "Accept:application/json" -H "subjectid:MYTOKEN" -d "geneIdentifiers=['entrez:3075']" https://services.toxbank.net/investigation/sparql/biosearch
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/sparql/investigations_and_factors
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/sparql/investigations_and_protocols
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' -d "factorValues=['http://purl.obolibrary.org/chebi/CHEBI:39867']" https://services.toxbank.net/investigation/sparql/protocols_by_factors

Links: Page, Edit with form



Create an investigation

Description Create a new investigation from ISA-TAB files
Resource Investigation
Method POST
URI /investigation
Parameters optional params:
  • allowReadByUser: one or multiple userservice-URIs (User)
  • allowReadByGroup: one or multiple userservice-URIs (Organisations, Projects)
  • summarySearchable: true/false (default is false)

required params (when upload not in isa-tab format):

  • type: one of noData/unformattedData/ftpData
  • title: string
  • abstract: string
  • owningOrg: one userservice-URI (Organisations)
  • owningPro: one or multiple userservice-URIs (Projects)
  • authors: one or multiple userservice-URIs (User)
  • keywords: one or multiple owl-URIs
  • ftpFile: one or multiple filenames (only for type ftpData)

optional params (when upload not in isa-tab format):

  • licenses: string
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input) multipart/form-data:
  • upload ISA-TAB files (isa-tab zip archive)
  • upload unformatted data (zip archive, required params)
  • upload without data (ftp filename, required params)
  • upload without data (required params)
Results Task URI
Media Type (output) text/uri-list
Status code 202, 400, 401

cURL example

curl -Lk -X POST -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \
https://services.toxbank.net/investigation?allowReadByUser=USER_URI1,USER_URI2&allowReadByGroup=GROUP_URI1,GROUP_URI2&summarySearchable=VALUE
curl -Lk -X POST -i -H "subjectid:MYTOKEN" -d "type=noData" -d "title=STRING" -d "abstract=STRING" -d "owningOrg=GROUP_URI" \ 
-d owningPro=GROUP_URI1,GROUP_URI2" -d "authors=USER_URI1,USER_URI2" -d "keywords=OWL_URI1,OWL_URI2" -d "allowReadByUser=USER_URI1,USER_URI2" \
-d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d "summarySearchable=VALUE" https://services.toxbank.net/investigation
curl -Lk -X POST -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \
https://services.toxbank.net/investigation?type=unformattedData&title=STRING&abstract=STRING&owningOrg=GROUP_URI&owningPro=GROUP_URI1,GROUP_URI2 \
&authors=USER_URI1,USER_URI2&keywords=OWL_URI1,OWL_URI2&allowReadByUser=USER_URI1,USER_URI2&allowReadByGroup=GROUP_URI1,GROUP_URI2 \
&summarySearchable=VALUE
curl -Lk -X POST -i -H "subjectid:MYTOKEN" -d "type=ftpData" -d "title=STRING" -d "abstract=STRING" -d "owningOrg=GROUP_URI" \
-d owningPro=GROUP_URI1,GROUP_URI2" -d "authors=USER_URI1,USER_URI2" -d "keywords=OWL_URI1,OWL_URI2" -d "licenses=STRING" \
-d "ftpFile=FILENAME_A,FILENAME_B" -d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" \
-d "summarySearchable=VALUE" https://services.toxbank.net/investigation

Links: Page, Edit with form


Get investigation data creation subtaskuri

Description Get investigation data subtask
Resource Investigation
Method GET
URI /investigation/{id}/subtaskuri
Parameters
Header Parameters Accept: text/uri-list or application/json, subjectid:SECURITY-TOKEN
Media Type (input)
Results SubTaskURI URI to task
Media Type (output) text/uri-list, application/json
Status code 200, 400, 401, 404

cURL example

curl -X GET -k -H 'Accept:text/uri-list' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/subtaskuri

Links: Page, Edit with form


Get an investigation representation

Description Get an investigation representation
Resource Investigation
Method GET
URI /investigation/{id}
Parameters
Header Parameters Accept: one of text/tab-separated-values, text/uri-list, application/zip, text/plain (n-triples), text/turtle, application/rdf+xml, subjectid:SECURITY-TOKEN
Media Type (input)
Results Investigation ISA-TAB file, list of study, assay and data URIs, zipped ISA-TAB files (including studies, assays and data files) or RDF representation
Media Type (output) text/tab-separated-values, text/uri-list, application/zip, text/plain, application/rdf+xml
Status code 200, 400, 401, 404

Links: Page, Edit with form


Get investigation metadata

Description Get investigation metadata
Resource Investigation
Method GET
URI /investigation/{id}/metadata
Parameters
Header Parameters Accept: one of text/plain (n-triples), text/turtle, application/rdf+xml, subjectid:SECURITY-TOKEN
Media Type (input)
Results Investigation metadata in n-triples, turtle or RDF format
Media Type (output) text/plain (n-triples), text/turtle, application/rdf+xml
Status code 200, 400, 401

Links: Page, Edit with form


cURL example

curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/metadata

Get investigation data

Description Get investigation data via predefined SPARQL templates
Resource Investigation
Method GET
URI /investigation/{id}/sparql/{template_name} or investigation/{id}/sparql/{template_name}/{biosample_id}
Parameters
Header Parameters Accept: one of < application/sparql-results+xml, application/json, text/uri-list, text/html > , subjectid:SECURITY-TOKEN
Media Type (input)
Results Investigation data as sparql-results+xml json uri-list html
Media Type (output) application/sparql-results+xml application/json text/uri-list text/html
Status code 200, 400, 401, 404

Get investigation data via predefined SPARQL templates. Add one of investigation_endpoint_technology, investigation_details, factors_by_investigation or characteristics_by_investigation to an investigation plus /sparql/ URI (e.G.: https://services.toxbank.net/investigation/{id}/sparql/investigation_endpoint_technology ) . You may also use camelcase notation for templatenames (e.G.: FactorsByInvestigation). Links: Page, Edit with form


cURL example

curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsByInvestigation
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/CharacteristicsBySample/{biosample}
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorsByInvestigation
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FactorvaluesByInvestigation
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesAndAssaysByInvestigation
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesByInvestigation
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/FilesWithDatanodesByInvestigation
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationDetails
curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/sparql/InvestigationEndpointTechnology

Get investigation data for dashboard contents

Description Get investigation data for GUI dashboard
Resource Investigation
Method GET
URI /investigation/{id}/dashboard
Parameters
Header Parameters Accept: application/json, subjectid:SECURITY-TOKEN
Media Type (input)
Results Investigation dashboard data as JSON
Media Type (output) application/json
Status code 200, 400, 401

Links: Page, Edit with form


cURL example

curl -X GET -k -H 'Accept:application/json' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/dashboard

Get an ISA-TAB entry

Description Get an ISA-TAB entry
Resource Investigation
Method GET
URI /investigation/{id}/{resource}
Parameters
Header Parameters Accept: one of text/plain (n-triples), text/turtle, application/rdf+xml, subjectid:SECURITY-TOKEN
Media Type (input)
Results Investigation ISA-TAB entry in n-triples, turtle or RDF format
Media Type (output) text/plain (n-triples), text/turtle, application/rdf+xml
Status code 200, 400, 401

Links: Page, Edit with form


cURL example

curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/MN20977

Delete an investigation

Description Delete an investigation
Resource Investigation
Method DELETE
URI /investigation/{id}
Parameters
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input)
Results Success message
Media Type (output) text/plain
Status code 200, 401

Links: Page, Edit with form


cURL example

curl -X DELETE -k -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}

Add/update studies, assays or data to an investigation

Description Add/update studies, assays or data to an investigation
Resource Investigation
Method PUT
URI /investigation/{id}
Parameters optional params:
  • allowReadByUser: one or multiple userservice-URIs (User)
  • allowReadByGroup: one or multiple userservice-URIs (Organisations, Projects)
  • summarySearchable: true/false (default is false)
  • published: true/false (default is false)

required params (when upload not in isa-tab format):

  • type: one of noData/unformattedData/ftpData
  • title: string
  • abstract: string
  • owningOrg: one userservice-URI (Organisations)
  • owningPro: one or multiple userservice-URIs (Projects)
  • authors: one or multiple userservice-URIs (User)
  • keywords: one or multiple owl-URIs
  • ftpFile: one or multiple filenames (only for type ftpData)
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input) multipart/form-data
Results Task URI
Media Type (output) text/uri-list
Status code 202, 400, 401, 423

Individual ISA-TAB files (text/tab-separated-values) or zip archives of study, assay and data files can be posted as form data to add files to an existing investigation. Investigations without ISA-TAB formated data can be edited by parameters and data files posted as form data replace existing data. Links: Page, Edit with form



cURL example

Add/update studies, assays or data to an investigation or update data

curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -F file="@ExampleFilename.zip;type=application/zip" \
-d "allowReadByUser=USER_URI1,USER_URI2" -d "allowReadByGroup=GROUP_URI1,GROUP_URI2" -d 'summarySearchable=VALUE' https://services.toxbank.net/investigation/{id}

Update isPublished flag in metadata

curl -Lk -X PUT -i -H "subjectid:MYTOKEN" -d "published=true" https://services.toxbank.net/investigation/{id}



Get a study, assay or data representation

Description Get a study, assay, data representation
Resource Investigation
Method GET
URI /investigation/{id}/isatab/{filename}
Parameters
Header Parameters subjectid:SECURITY-TOKEN
Media Type (input)
Results Study, assay, data representation in ISA-TAB format
Media Type (output) text/tab-separated-values
Status code 200, 400, 401, 404

Links: Page, Edit with form



Get a protocol uri associated with a Study

Description Get a study related protocol uri
Resource Investigation
Method GET
URI /investigation/{id}/protocol
Parameters
Header Parameters Subjectid:SECURITY-TOKEN
Media Type (input) Accept:application/rdf+xml
Results Protocol uris
Media Type (output) application/rdf+xml
Status code 200, 400, 401, 404

Links: Page, Edit with form


cURL example

curl -X GET -k -H 'Accept:application/rdf+xml' -H 'subjectid:MYTOKEN' https://services.toxbank.net/investigation/{id}/protocol


Security

see Protocol

Investigation metadata in RDF

Investigation

Namespace: tbisa: http://onto.toxbank.net/isa

Class

   <investigation_uri>   a   tbisa:Investigation.

Data properties

   tbisa:hasAccessionID  "String" .
   dcterms:title "String".
   dcterms:abstract  "String".
   dcterms:created "Date". 
   dcterms:issued  "Date".
  

Object properties:

   tbisa:hasStudy rdfs:domain tbisa:Investigation . 
   tbisa:hasStudy rdfs:range tbisa:Study . 
   tbisa:hasOwner rdfs:range tbisa:Contact .

Example N3

@prefix dc: <http://purl.org/dc/terms/> . @prefix ot: <http://www.opentox.org/api/1.2#> . @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

<investigation_uri> a <http://onto.toxbank.net/isa/Investigation>,

    ot:Investigation;
  dc:title "TG Gate: The Toxicogenomics Project";
  <http://onto.toxbank.net/api/hasKeyword> "http://www.owl-ontologies.com/toxbank.owl/K169",
    "http://www.owl-ontologies.com/toxbank.owl/K223",
    "http://www.owl-ontologies.com/toxbank.owl/K9",
    "http://www.owl-ontologies.com/toxbank.owl/K348";
  <http://onto.toxbank.net/api/hasOrganisation> <service_uri/organisation/G33>,
    <service_uri/organisation/G20>;
  <http://onto.toxbank.net/api/hasOwner> <service_uri/user/U271>;
  <http://onto.toxbank.net/api/hasProject> <service_uri/project/G17>;
  <http://onto.toxbank.net/api/isPublished> false;
  <http://onto.toxbank.net/api/isSummarySearchable> false;
  <http://onto.toxbank.net/isa/hasStudy> <investigation_uri/S1>;
  dc:abstract "TGGATE dataset is a toxicogenomics dataset generated through the Toxicogenomics Project. The Toxicogenomics Project ... ";
  dc:modified "19 May 2014 12:24:58 IST" .

Study

Class

   <study_uri>   a   tbisa:Study.

Data properties

   tbisa:hasAccessionID  "String" .
   dcterms:title "String".
   dcterms:description  "String".
   dcterms:created "Date". 
  

Object properties:

   tbisa:hasAssay rdfs:domain tbisa:Study . 
   tbisa:hasAssay rdfs:range tbisa:Assay . 
   tbisa:hasProtocol rdfs:domain tbisa:Study . 
   tbisa:hasProtocol rdfs:range tbisa:Protocol . 
   tbisa:hasOwner rdfs:range tbisa:Contact .

Example N3

<http://onto.toxbank.net/isa/BIII1/S1138>
     a       tbisa:Study ;
     tbisa:hasAccessionID
             "BII-S-2" ;
     tbisa:hasAssay <http://onto.toxbank.net/isa/BIII1/A1037> , <http://onto.toxbank.net/isa/BIII1/A1055>   ;
     tbisa:hasOwner <http://onto.toxbank.net/isa/BIII1/ISA_1137> , <http://onto.toxbank.net/isa/BIII1/ISA_3982> ;
     tbisa:hasProtocol <http://onto.toxbank.net/isa/BIII1/P_10> , <http://onto.toxbank.net/isa/BIII1/P_18>  ;
     dcterms:created "29 Apr 2007 21:00:00 GMT" ;
     dcterms:description "Comprehensive high-throughput analyses .... (skipped) ." ;
     dcterms:title "A time course analysis of  transcription response in yeast treated with rapamycin, a specific inhibitor of the TORC1 complex: impact on yeast growth" .
<http://onto.toxbank.net/isa/BIII1/PA2538>
     a       tbisa:ProtocolApplication ;
     tbisa:appliesProtocol
             <http://onto.toxbank.net/isa/BIII1/P_10> .

Protocol

Class

   <protocol_uri>   a   tbisa:Protocol , tb:Protocol;

Data properties

   tbisa:hasAccessionID  "String" .
   dcterms:title "String".. 
  

Object properties:

tbisa:appliesProtocol
     a       owl:FunctionalProperty , owl:ObjectProperty ;
     rdfs:domain tbisa:ProtocolApplication ;
     rdfs:range tbisa:Protocol .
tbisa:hasProtocol
     a       owl:ObjectProperty ;
     rdfs:domain tbisa:Study ;
     rdfs:range tbisa:Protocol .
tbisa:appliesProtocol
     a       owl:FunctionalProperty , owl:ObjectProperty ;
     rdfs:domain tbisa:ProtocolApplication ;
     rdfs:range tbisa:Protocol .
tbisa:hasParameterValue
     a       owl:ObjectProperty ;
     rdfs:domain tbisa:ProtocolApplication ;
     rdfs:range tbisa:ParameterValue .
tbisa:hasProtocolApplication
     a       owl:ObjectProperty ;
     rdfs:domain tbisa:Processing ;
     rdfs:range tbisa:ProtocolApplication .

Example N3

<http://onto.toxbank.net/isa/BIII1/P_17>
     a       tbisa:Protocol ;
     rdfs:label "mRNA  extraction"^^<http://www.w3.org/2001/XMLSchema#string> ;
     tbisa:hasAccessionID
             "BII-S-2\\mRNA  extraction" .

Contact (Person, User )

Classes

   <person_uri>  a   foaf:Person , tbisa:Contact , tb:User ;

Data properties

   (as for tb:User -   foaf:family_name,  foaf:givenname , etc.)
  

Object properties:

  tbisa:hasOwner  rdfs:range tbisa:Contact .

Example N3

<http://onto.toxbank.net/isa/BIII1/ISA_3980>
     a       foaf:Person , tbisa:Contact , tb:User ;
     foaf:family_name "Oliver"^^<http://www.w3.org/2001/XMLSchema#string> ;
     foaf:givenname "Stephen"^^<http://www.w3.org/2001/XMLSchema#string> .


Processing node

Classes

   <processingnode>  a   tbisa: Processing;

Subclasses

tbisa:DataProcessing
     rdfs:subClassOf tbisa:Processing .
tbisa:MaterialProcessing
     rdfs:subClassOf tbisa:Processing .
tbisa:DataAcquisition
     rdfs:subClassOf tbisa:Processing .
  

Object properties:

tbisa:hasProtocolApplication
     a       owl:ObjectProperty ;
     rdfs:domain tbisa:Processing ;
     rdfs:range tbisa:ProtocolApplication .
tbisa:hasInputNode
     a       owl:ObjectProperty ;
     rdfs:domain tbisa:Processing ;
     rdfs:range tbisa:Node .
tbisa:hasOutputNode
     a       owl:ObjectProperty ;
     rdfs:domain tbisa:Processing ;
     rdfs:range tbisa:Node .
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