From 0a65b6ac82407093fe4e888e91e6266558f201bc Mon Sep 17 00:00:00 2001 From: Florian Wetzels Date: Mon, 18 Dec 2023 16:04:50 +0100 Subject: [PATCH 1/4] initial type draft for LabProcess --- LabProcess/README.md | 12 ++++ .../jsonld/type/LabProcess_v0.1-DRAFT.jsonld | 62 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 LabProcess/README.md create mode 100644 LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld diff --git a/LabProcess/README.md b/LabProcess/README.md new file mode 100644 index 0000000..d47ffc9 --- /dev/null +++ b/LabProcess/README.md @@ -0,0 +1,12 @@ +# LabProcess Specification + +## Type + +Thing > CreativeWork > [LabProcess](https://bioschemas.org/LabProcess/) + +## Profile + +### Example Markup + +## Issue Tracker + diff --git a/LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld b/LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld new file mode 100644 index 0000000..367d95a --- /dev/null +++ b/LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld @@ -0,0 +1,62 @@ +{ + "@context": { + "schema": "http://schema.org/", + "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "isa": "https://discovery.biothings.io/view/isa/", + "bioschemas": "https://discovery.biothings.io/view/bioschemas/" + }, + "@graph": [ + { + "@id": "isa:LabProcess", + "@type": "rdfs:Class", + "rdfs:comment": "This is an initial draft of the new LabProcess type.\n\nA LabProcess represents the specific application of a LabProtocol to some input (biological material or data) to produce some output (biological material or data).\n\nThis draft was prepared by Florian Wetzels and Lukas Weil, its specification is still up for discussion.", + "rdfs:label": "LabProcess", + "rdfs:subClassOf": { + "@id": "schema:Action" + }, + "$validation": { + "$schema": "http://json-schema.org/draft-07/schema#", + "type": "object", + "properties": { + "parameterValue": { + "description": "A parameter value of the experimental process, usually a key-value pair using ontology terms." + }, + "executesLabProtocol": { + "description": "The protocol describes the experimental workflow and its parameters, which is instanciated by this process." + } + }, + "required": [], + "recommended": [], + "optional": [] + }, + "schemaVersion": [ + "https://schema.org/docs/releases.html#v23.0" + ] + }, + { + "@id": "isa:parameterValue", + "@type": "rdf:Property", + "rdfs:comment": "A parameter value of the experimental process, usually a key-value pair using ontology terms.", + "rdfs:label": "parameterValue", + "schema:domainIncludes": "isa:LabProcess", + "schema:rangeIncludes": [ + { + "@id": "schema:PropertyValue" + } + ] + }, + { + "@id": "isa:executesLabProtocol", + "@type": "rdf:Property", + "rdfs:comment": "The protocol describes the experimental workflow and its parameters, which is instanciated by this process.", + "rdfs:label": "executesLabProtocol", + "schema:domainIncludes": "isa:LabProcess", + "schema:rangeIncludes": [ + { + "@id": "bioschemastypesdrafts:LabProtocol" + } + ] + } + ] +} \ No newline at end of file From af4b8f13e36597fa8c786dc04a75e11ec1bc32ac Mon Sep 17 00:00:00 2001 From: Dominik Brilhaus Date: Thu, 4 Jan 2024 08:49:22 +0100 Subject: [PATCH 2/4] small suggestion and fix typo --- LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld b/LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld index 367d95a..8f4fe5a 100644 --- a/LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld +++ b/LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld @@ -23,7 +23,7 @@ "description": "A parameter value of the experimental process, usually a key-value pair using ontology terms." }, "executesLabProtocol": { - "description": "The protocol describes the experimental workflow and its parameters, which is instanciated by this process." + "description": "The lab protocol describes the experimental workflow and its parameters, which is instantiated by this process." } }, "required": [], @@ -49,7 +49,7 @@ { "@id": "isa:executesLabProtocol", "@type": "rdf:Property", - "rdfs:comment": "The protocol describes the experimental workflow and its parameters, which is instanciated by this process.", + "rdfs:comment": "The lab protocol describes the experimental workflow and its parameters, which is instantiated by this process.", "rdfs:label": "executesLabProtocol", "schema:domainIncludes": "isa:LabProcess", "schema:rangeIncludes": [ From ac54cd17d8ea7fa778b4f1075c294a711b0c5d95 Mon Sep 17 00:00:00 2001 From: Florian Wetzels Date: Fri, 5 Jan 2024 15:32:02 +0100 Subject: [PATCH 3/4] fixed bug in LabProcess type draft and added example for LabProcess/LabProtocol --- .../examples/0.1-DRAFT/labprocess_v0.1.json | 85 +++++++++++++++++++ .../jsonld/type/LabProcess_v0.1-DRAFT.jsonld | 31 +++---- 2 files changed, 95 insertions(+), 21 deletions(-) create mode 100644 LabProcess/examples/0.1-DRAFT/labprocess_v0.1.json diff --git a/LabProcess/examples/0.1-DRAFT/labprocess_v0.1.json b/LabProcess/examples/0.1-DRAFT/labprocess_v0.1.json new file mode 100644 index 0000000..bf046ad --- /dev/null +++ b/LabProcess/examples/0.1-DRAFT/labprocess_v0.1.json @@ -0,0 +1,85 @@ +{ + "@context": "http://schema.org/", + "@type": [ + "LabProcess" + ], + "name": "Cell Cultivation", + "executesProtocol": { + "@type": [ + "LabProtocol" + ], + "intendedUse": { + "@type": "DefinedTerm", + "name": "growth protocol", + "termCode": "http://purl.obolibrary.org/obo/EFO_0003789" + }, + "labEquipment": { + "@type": [ + "DefinedTerm" + ], + "alternateName": "Fisherbrand™ Model 705 Sonic Dismembrator ()", + "name": "sonicator", + "termCode": "OBI:0400114", + "disambiguatingDescription": [ + "ColumnIndex:1" + ] + }, + "url": "abc.de", + "version": "1" + }, + "parameterValue": [ + { + "@type": "PropertyValue", + "name": "temperature", + "value": "20", + "unitCode": "http://purl.obolibrary.org/obo/UO_0000027", + "unitText": "degree Celsius", + "propertyID": "http://purl.obolibrary.org/obo/PATO_0000146" + }, + { + "@type": "PropertyValue", + "name": "organism", + "value": "Arabidopsis thaliana", + "propertyID": "http://purl.obolibrary.org/obo/OBI_0100026", + "valueReference": "http://purl.obolibrary.org/obo/NCBITaxon_3702" + } + ], + "agent": { + "@type": "Person", + "givenName": "Timo", + "familyName": "Mühlhaus" + }, + "endTime": "2012-04-23T18:25:43.511Z", + "object": [ + { + "@type": [ + "Sample" + ], + "name": "Sample1", + "additionalProperties": [] + }, + { + "@type": [ + "Sample" + ], + "name": "Sample2", + "additionalProperties": [] + } + ], + "result": [ + { + "@type": [ + "Sample" + ], + "name": "Cultivation Flask", + "additionalProperties": [] + }, + { + "@type": [ + "Sample" + ], + "name": "Cultivation Flask", + "additionalProperties": [] + } + ] +} \ No newline at end of file diff --git a/LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld b/LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld index 367d95a..fe162a8 100644 --- a/LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld +++ b/LabProcess/jsonld/type/LabProcess_v0.1-DRAFT.jsonld @@ -3,43 +3,30 @@ "schema": "http://schema.org/", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "isa": "https://discovery.biothings.io/view/isa/", + "bioschemastypesdrafts": "https://discovery.biothings.io/view/bioschemastypesdrafts/", "bioschemas": "https://discovery.biothings.io/view/bioschemas/" }, "@graph": [ { - "@id": "isa:LabProcess", + "@id": "bioschemastypesdrafts:LabProcess", "@type": "rdfs:Class", "rdfs:comment": "This is an initial draft of the new LabProcess type.\n\nA LabProcess represents the specific application of a LabProtocol to some input (biological material or data) to produce some output (biological material or data).\n\nThis draft was prepared by Florian Wetzels and Lukas Weil, its specification is still up for discussion.", "rdfs:label": "LabProcess", "rdfs:subClassOf": { "@id": "schema:Action" }, - "$validation": { - "$schema": "http://json-schema.org/draft-07/schema#", - "type": "object", - "properties": { - "parameterValue": { - "description": "A parameter value of the experimental process, usually a key-value pair using ontology terms." - }, - "executesLabProtocol": { - "description": "The protocol describes the experimental workflow and its parameters, which is instanciated by this process." - } - }, - "required": [], - "recommended": [], - "optional": [] - }, "schemaVersion": [ "https://schema.org/docs/releases.html#v23.0" ] }, { - "@id": "isa:parameterValue", + "@id": "bioschemastypesdrafts:parameterValue", "@type": "rdf:Property", "rdfs:comment": "A parameter value of the experimental process, usually a key-value pair using ontology terms.", "rdfs:label": "parameterValue", - "schema:domainIncludes": "isa:LabProcess", + "schema:domainIncludes": { + "@id": "bioschemastypesdrafts:LabProcess" + }, "schema:rangeIncludes": [ { "@id": "schema:PropertyValue" @@ -47,11 +34,13 @@ ] }, { - "@id": "isa:executesLabProtocol", + "@id": "bioschemastypesdrafts:executesLabProtocol", "@type": "rdf:Property", "rdfs:comment": "The protocol describes the experimental workflow and its parameters, which is instanciated by this process.", "rdfs:label": "executesLabProtocol", - "schema:domainIncludes": "isa:LabProcess", + "schema:domainIncludes": { + "@id": "bioschemastypesdrafts:LabProcess" + }, "schema:rangeIncludes": [ { "@id": "bioschemastypesdrafts:LabProtocol" From 26fdfb0676f336f28e932cbb1cfd890b1110e9e2 Mon Sep 17 00:00:00 2001 From: Heinrich Lukas Weil Date: Thu, 11 Jan 2024 11:22:24 +0100 Subject: [PATCH 4/4] extend labprocess_0.1-DRAFT example --- .../examples/0.1-DRAFT/labprocess_v0.1.json | 110 ++++++++++++++---- 1 file changed, 88 insertions(+), 22 deletions(-) diff --git a/LabProcess/examples/0.1-DRAFT/labprocess_v0.1.json b/LabProcess/examples/0.1-DRAFT/labprocess_v0.1.json index bf046ad..3e579ac 100644 --- a/LabProcess/examples/0.1-DRAFT/labprocess_v0.1.json +++ b/LabProcess/examples/0.1-DRAFT/labprocess_v0.1.json @@ -17,15 +17,10 @@ "@type": [ "DefinedTerm" ], - "alternateName": "Fisherbrand™ Model 705 Sonic Dismembrator ()", - "name": "sonicator", - "termCode": "OBI:0400114", - "disambiguatingDescription": [ - "ColumnIndex:1" - ] - }, - "url": "abc.de", - "version": "1" + "alternateName": "Photon System Instruments, FMT 150/400-RB", + "name": "bioreactor", + "termCode": "http://purl.obolibrary.org/obo/OBI_0001046" + } }, "parameterValue": [ { @@ -38,16 +33,31 @@ }, { "@type": "PropertyValue", - "name": "organism", - "value": "Arabidopsis thaliana", - "propertyID": "http://purl.obolibrary.org/obo/OBI_0100026", - "valueReference": "http://purl.obolibrary.org/obo/NCBITaxon_3702" - } + "name": "culture medium volume", + "value": "400", + "unitCode": "http://purl.obolibrary.org/obo/UO_0000098", + "unitText": "milliliter", + "propertyID": "DPBO:1000155" + }, + { + "@type": "PropertyValue", + "name": "Mixture Component", + "value": "TAP medium", + "propertyID": "http://purl.obolibrary.org/obo/NCIT_C103243" + }, + { + "@type": "PropertyValue", + "name": "light intensity", + "value": "400", + "unitCode": "http://purl.obolibrary.org/obo/UO_0000160", + "unitText": "microeinstein per square meter per second", + "propertyID": "http://purl.obolibrary.org/obo/ZECO_0000151" + } ], "agent": { "@type": "Person", - "givenName": "Timo", - "familyName": "Mühlhaus" + "givenName": "Benedikt", + "familyName": "Venn" }, "endTime": "2012-04-23T18:25:43.511Z", "object": [ @@ -55,15 +65,64 @@ "@type": [ "Sample" ], - "name": "Sample1", - "additionalProperties": [] + "name": "reactor_35_A", + "additionalProperties": [ + { + "@type": "PropertyValue", + "name": "organism", + "value": "Chlamydomonas reinhardtii", + "propertyID": "http://purl.obolibrary.org/obo/OBI_0100026", + "valueReference": "http://purl.obolibrary.org/obo/NCBITaxon_3055" + }, + { + "@type": "PropertyValue", + "name": "biological replicate", + "value": 1, + "propertyID": "http://www.ebi.ac.uk/efo/EFO_0002091" + } + ] }, { "@type": [ "Sample" ], - "name": "Sample2", - "additionalProperties": [] + "name": "reactor_35_B", + "additionalProperties": [ + { + "@type": "PropertyValue", + "name": "organism", + "value": "Chlamydomonas reinhardtii", + "propertyID": "http://purl.obolibrary.org/obo/OBI_0100026", + "valueReference": "http://purl.obolibrary.org/obo/NCBITaxon_3055" + }, + { + "@type": "PropertyValue", + "name": "biological replicate", + "value": 2, + "propertyID": "http://www.ebi.ac.uk/efo/EFO_0002091" + } + ] + }, + { + "@type": [ + "Sample" + ], + "name": "reactor_35_C", + "additionalProperties": [ + { + "@type": "PropertyValue", + "name": "organism", + "value": "Chlamydomonas reinhardtii", + "propertyID": "http://purl.obolibrary.org/obo/OBI_0100026", + "valueReference": "http://purl.obolibrary.org/obo/NCBITaxon_3055" + }, + { + "@type": "PropertyValue", + "name": "biological replicate", + "value": 3, + "propertyID": "http://www.ebi.ac.uk/efo/EFO_0002091" + } + ] } ], "result": [ @@ -71,14 +130,21 @@ "@type": [ "Sample" ], - "name": "Cultivation Flask", + "name": "run_35_A", + "additionalProperties": [] + }, + { + "@type": [ + "Sample" + ], + "name": "run_35_B", "additionalProperties": [] }, { "@type": [ "Sample" ], - "name": "Cultivation Flask", + "name": "run_35_C", "additionalProperties": [] } ]