Skip to content

Commit

Permalink
Release version
Browse files Browse the repository at this point in the history
  • Loading branch information
y25ean committed Jun 12, 2019
1 parent 703e3af commit e418ee5
Show file tree
Hide file tree
Showing 130 changed files with 23,744 additions and 16,253 deletions.
297 changes: 87 additions & 210 deletions Scripting-Tool/draft-profiles/ChemicalSubstance.json

Large diffs are not rendered by default.

271 changes: 74 additions & 197 deletions Scripting-Tool/draft-profiles/Gene.json

Large diffs are not rendered by default.

271 changes: 74 additions & 197 deletions Scripting-Tool/draft-profiles/LabProtocol.json

Large diffs are not rendered by default.

271 changes: 74 additions & 197 deletions Scripting-Tool/draft-profiles/MolecularEntity.json

Large diffs are not rendered by default.

5 changes: 0 additions & 5 deletions Scripting-Tool/draft-profiles/Organization.json

This file was deleted.

5 changes: 0 additions & 5 deletions Scripting-Tool/draft-profiles/Person.json

This file was deleted.

271 changes: 74 additions & 197 deletions Scripting-Tool/draft-profiles/Phenotype.json

Large diffs are not rendered by default.

271 changes: 74 additions & 197 deletions Scripting-Tool/draft-profiles/Protein.json

Large diffs are not rendered by default.

271 changes: 74 additions & 197 deletions Scripting-Tool/draft-profiles/ProteinAnnotation.json

Large diffs are not rendered by default.

271 changes: 74 additions & 197 deletions Scripting-Tool/draft-profiles/ProteinStructure.json

Large diffs are not rendered by default.

5 changes: 0 additions & 5 deletions Scripting-Tool/draft-profiles/Standard.json

This file was deleted.

39 changes: 1 addition & 38 deletions Scripting-Tool/draft-tables/Beacon-Table.json
Original file line number Diff line number Diff line change
@@ -1,38 +1 @@
{
"aggregator": {
"marginality": "Recommended"
},
"dataset": {
"marginality": "Minimum"
},
"description": {
"marginality": "Recommended"
},
"identifier": {
"marginality": "Recommended"
},
"name": {
"marginality": "Minimum"
},
"potentialAction": {
"marginality": "Minimum"
},
"provider": {
"marginality": "Minimum"
},
"rdf:type": {
"marginality": "Minimum"
},
"sameAs": {
"marginality": "Optional"
},
"supportedRefs": {
"marginality": "Minimum"
},
"url": {
"marginality": "Minimum"
},
"version": {
"marginality": "Recommended"
}
}
{}
15 changes: 0 additions & 15 deletions Scripting-Tool/draft-tables/ChemicalSubstance-Table.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,12 +3,6 @@
"example": "\"alternateName\": [\n \"SiO2\"\n]",
"marginality": "Optional"
},
"biochemicalInteraction": {
"marginality": "Optional"
},
"biochemicalSimilarity ": {
"marginality": "Optional"
},
"biologicalRole": {
"controlled_vocab": "Any suitable ontology such as [ChEBI biological role](https://www.ebi.ac.uk/ols/ontologies/chebi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_24432)",
"marginality": "Optional"
Expand All @@ -18,12 +12,6 @@
"controlled_vocab": "Any suitable ontology such as [ChEBI Chemical Role](https://www.ebi.ac.uk/ols/ontologies/chebi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_51086)",
"marginality": "Optional"
},
"description": {
"marginality": "Optional"
},
"disambiguatingDescription": {
"marginality": "Optional"
},
"hasBioChemEntityPart": {
"example": "\"hasBioChemEntityPart\": [{\n \"@type\": \"BioChemEntity\",\n \"identifier\": \"CHEBI:30563\",\n \"name\": \"silicon dioxide\",\n \"url\": \"https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:30563\"\n}]",
"marginality": "Recommended"
Expand All @@ -32,9 +20,6 @@
"example": "\"identifier\": \"https://data.enanomapper.net/substance/NWKI-e624f68e-2e00-30e4-b4bb-9e34383580cb/study\"",
"marginality": "Minimum"
},
"image": {
"marginality": "Optional"
},
"molecularFormula": {
"example": "\"molecularFormula\": \"SiO2\"",
"marginality": "Recommended"
Expand Down
21 changes: 0 additions & 21 deletions Scripting-Tool/draft-tables/Course-Table.json
Original file line number Diff line number Diff line change
Expand Up @@ -12,25 +12,10 @@
"example": "\"accessibilitySummary\": \"Visual elements are not described.\"\n",
"marginality": "Optional"
},
"aggregateRating": {
"marginality": "Recommended"
},
"alternateName": {
"example": "\"alternateName\": [\"Comp-sci 101\"]",
"marginality": "Optional"
},
"citation": {
"marginality": "Recommended"
},
"comment": {
"marginality": "Optional"
},
"commentCount": {
"marginality": "Optional"
},
"contentReferenceTime": {
"marginality": "Optional"
},
"courseCode": {
"example": "\"courseCode\": \"CS101\"",
"marginality": "Optional"
Expand Down Expand Up @@ -71,9 +56,6 @@
"example": "\"image\": \"https://image.server.com/my-image.jpg\"",
"marginality": "Optional"
},
"isBasedOn": {
"marginality": "Optional"
},
"keywords": {
"example": "\"keywords\": \"RNA-Seq, Workshop\"",
"marginality": "Minimum"
Expand All @@ -83,9 +65,6 @@
"controlled_vocab": "It is recommended you utilize terms from Blooms taxonomy",
"marginality": "Optional"
},
"license": {
"marginality": "Recommended"
},
"mentions": {
"example": "\"mentions\": [{\n \"@type\": \"Tool\",\n \"name\": \"Galaxy\",\n \"url\": \"https://bio.tools/galaxy\",\n \"description\": \"Open, web-based platform for data intensive biomedical research\"\n},{\n \"@type\": \"Dataset\",\n \"name\": \"European Genome-phenome Archive\",\n \"url\": \"https://www.ebi.ac.uk/ega/home\",\n \"description\": \"The EGA archives a large number of datasets, the access to which is controlled by a Data Access Committee (DAC).\"\n}]",
"marginality": "Recommended"
Expand Down
3 changes: 0 additions & 3 deletions Scripting-Tool/draft-tables/CourseInstance-Table.json
Original file line number Diff line number Diff line change
Expand Up @@ -75,9 +75,6 @@
"example": "\"organizer\": [{\n \"@type\": \"Person\",\n \"name\": \"Elizabeth Windsor\",\n \"email\": \"[email protected]\"\n},{ \n \"@type\": \"Organization\",\n \"name\": \"University of Manchester\"\n}]",
"marginality": "Optional"
},
"review": {
"marginality": "Optional"
},
"startDate": {
"example": "\"startDate\": \"2019-02-04T09:00:00\"",
"controlled_vocab": "ISO 8601",
Expand Down
18 changes: 0 additions & 18 deletions Scripting-Tool/draft-tables/DataCatalog-Table.json
Original file line number Diff line number Diff line change
@@ -1,7 +1,4 @@
{
"about": {
"marginality": "Recommended"
},
"alternateName": {
"example": "{\n\"@type\": \"DataCatalog\",\n\"alternateName\": \"Reactome Pathway Database\"\n}",
"marginality": "Recommended"
Expand All @@ -10,22 +7,10 @@
"example": "{\n\"@type\": \"DataCatalog\",\n\"citation\": {\n \"@type\": \"ScholarlyArticle\",\n \"headline\": \"The Reactome pathway knowledgebase.\",\n \"identifier\": [\n \"http://identifiers.org/pubmed/24243840\"\n ],\n \"datePublished\": \"2015-11\"\n }\n}",
"marginality": "Recommended"
},
"dataset": {
"marginality": "Recommended"
},
"dateCreated": {
"marginality": "Recommended"
},
"dateModified": {
"marginality": "Optional"
},
"description": {
"example": "{\n\"@type\": \"DataCatalog\",\n \"description\": \"The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.\"\n}",
"marginality": "Minimum"
},
"encodingFormat": {
"marginality": "Optional"
},
"identifier": {
"example": "{\n\"@type\": \"DataCatalog\",\n\"identifier\": \"MIR:00000018\"\n}",
"marginality": "Recommended"
Expand All @@ -46,9 +31,6 @@
"example": "{\n \"@type\": \"DataCatalog\",\n \"provider\": {\n \"@type\": \"Organization\",\n \"name\": \"EMBL-EBI\",\n \"url\": \"https://www.ebi.ac.uk\"\n }\n}",
"marginality": "Minimum"
},
"sourceOrganization": {
"marginality": "Recommended"
},
"url": {
"example": "{\n\"@type\": \"DataCatalog\",\n\"url\": \"https://www.reactome.org/\"\n}",
"marginality": "Minimum"
Expand Down
45 changes: 0 additions & 45 deletions Scripting-Tool/draft-tables/DataRecord-Table.json
Original file line number Diff line number Diff line change
@@ -1,55 +1,10 @@
{
"additionalProperty": {
"marginality": "Optional"
},
"additionalType": {
"marginality": "Recommended"
},
"citation": {
"marginality": "Optional"
},
"dateCreated": {
"marginality": "Optional"
},
"dateModified": {
"marginality": "Optional"
},
"datePublished": {
"marginality": "Optional"
},
"distribution": {
"marginality": "Optional"
},
"identifier": {
"marginality": "Minimum"
},
"image": {
"marginality": "Optional"
},
"isBasedOn": {
"controlled_vocab": "[ECO](https://www.ebi.ac.uk/ols/ontologies/eco)",
"marginality": "Optional"
},
"isBasisFor": {
"controlled_vocab": "[ECO](https://www.ebi.ac.uk/ols/ontologies/eco)",
"marginality": "Optional"
},
"keywords": {
"marginality": "Optional"
},
"mainEntity": {
"marginality": "Minimum"
},
"rdf:type": {
"marginality": "Minimum"
},
"sameAs": {
"marginality": "Optional"
},
"seeAlso": {
"marginality": "Optional"
},
"url": {
"marginality": "Optional"
}
}
84 changes: 0 additions & 84 deletions Scripting-Tool/draft-tables/Event-Table.json
Original file line number Diff line number Diff line change
@@ -1,106 +1,22 @@
{
"acceptanceNotificationDate": {
"marginality": "Optional"
},
"accreditation": {
"marginality": "Recommended"
},
"alternateName": {
"marginality": "Recommended"
},
"attachment": {
"marginality": "Optional"
},
"audience": {
"controlled_vocab": "[EDAM: Topic](http://edamontology.org/topic_0003)",
"marginality": "Recommended"
},
"contact": {
"marginality": "Minimum"
},
"dateModified": {
"marginality": "Optional"
},
"deadline": {
"marginality": "Recommended"
},
"description": {
"marginality": "Minimum"
},
"eligibility": {
"controlled_vocab": "- first come first served\n- registration of interest\n- by invitation",
"marginality": "Recommended"
},
"endDate": {
"marginality": "Minimum"
},
"eventType": {
"controlled_vocab": "- workshops and courses\n- meetings and conferences\n- receptions and networking\n- awards and prizegivings",
"marginality": "Minimum"
},
"hostInstitution": {
"marginality": "Minimum"
},
"identifier": {
"marginality": "Optional"
},
"keywords": {
"marginality": "Recommended"
},
"location": {
"marginality": "Minimum"
},
"maximumAttendeeCapacity": {
"marginality": "Recommended"
},
"name": {
"marginality": "Minimum"
},
"offers": {
"marginality": "Optional"
},
"performer": {
"marginality": "Optional"
},
"prerequisite": {
"marginality": "Recommended"
},
"programme": {
"marginality": "Recommended"
},
"rdf:type": {
"marginality": "Minimum"
},
"registrationStatus": {
"controlled_vocab": "- proposed\n- pre-open\n- open\n- cancelled\n- full",
"marginality": "Optional"
},
"review": {
"marginality": "Optional"
},
"socialMedia": {
"marginality": "Optional"
},
"sponsor": {
"marginality": "Optional"
},
"startDate": {
"marginality": "Minimum"
},
"subEvent": {
"marginality": "Optional"
},
"submitter": {
"marginality": "Optional"
},
"superEvent": {
"marginality": "Optional"
},
"topic": {
"controlled_vocab": "[EDAM: Topic](http://edamontology.org/topic_0003)",
"marginality": "Recommended"
},
"url": {
"marginality": "Recommended"
}
}
12 changes: 0 additions & 12 deletions Scripting-Tool/draft-tables/Gene-Table.json
Original file line number Diff line number Diff line change
@@ -1,7 +1,4 @@
{
"additionalProperty": {
"marginality": "Optional"
},
"additionalType": {
"example": "{\n \"@type\": [\"Gene\"],\n \"additionalType\": \"http://semanticscience.org/resource/SIO_010035\"\n}",
"marginality": "Optional"
Expand All @@ -10,9 +7,6 @@
"example": "{\n \"@type\": [\"Gene\"],\n \"alternateName\": \"AD1\"\n}",
"marginality": "Optional"
},
"associatedDisease": {
"marginality": "Optional"
},
"description": {
"example": "{\n \"@type\": [\"Gene\"],\n \"description\": \"amyloid beta precursor\"\n}",
"marginality": "Recommended"
Expand All @@ -31,9 +25,6 @@
"example": "//Contains a variant\n{\n \"@type\": [\"Gene\"],\n \"hasBioChemEntityPart\": { \n \"@type\": \"BioChemEntity\",\n \"additionalType\": \"http://semanticscience.org/resource/SIO_001381\",\n \"identifier\": \"rs577882423\",\n },\n \"url\": \"https://www.ensembl.org/Homo_sapiens/Variation/Summary?db=core;g=ENSG00000142192;r=21:25880550-26171128;vf=110312838\"\n }\n}\n",
"marginality": "Optional"
},
"hasCategoryCode": {
"marginality": "Optional"
},
"hasRepresentation": {
"example": "{\n \"@type\": [\"Gene\"],\n \"hasRepresentation\": \"https://www.ncbi.nlm.nih.gov/nuccore/NC_000021.9?report=fasta&from=25880550&to=26171128&strand=true\"\n}",
"marginality": "Recommended"
Expand Down Expand Up @@ -76,9 +67,6 @@
"example": "{\n \"@type\": [\"Gene\"],\n \"sameAs\": \"https://www.wikidata.org/wiki/Q14865870\"\n}",
"marginality": "Optional"
},
"taxonomicRange": {
"marginality": "Optional"
},
"url": {
"example": "{\n \"@type\": [\"Gene\"],\n \"url\": \"https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000142192;r=21:25880550-26171128\"\n}",
"marginality": "Recommended"
Expand Down
Loading

0 comments on commit e418ee5

Please sign in to comment.