Bring proposed Bioschemas terms into Pending area #2862
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* Create BiologicalEntity class. Not as an extension yet... * Started drafting BioChemEntity type * Add BioChemEntity properties * Add ChemicalSubstance * Add DNA * Add gene * Fix typos * Add enzyme type * Add molecular entity * Add dot at the end of comments And fix hasSequence domains and ranges * Add protein type and properties * Add RNA * Add sequence annotation and missing property sources * Add sequence range * Add sequence range * change number to toext for temperature so the unit can be included as well * Add temperature comment * Change molecular weigth to text so the unit can be specified * Specializes some Number ranges * Add phenotype * Add range to expressedIn * Add protein structure adjusting domains and ranges when needed. And updating temperature range from Text to Quantity * Add lab protocol * Add interpro entries (sequence matching model) and add inverseOf statements and links * Enabled bio extension Commented out classes that fail to work * Removed old definition of BiologicalEntity * Fixed issues with Enzyme - Tweaks to wording of terms - Fixes to make valid HTML - Omitting keywords property * Fixes in HTML syntax to make MolecularEntity display * Fixed html syntax * Fixed #263 by correcting HTML * Fixed HTML syntax issues * Fixed typo * Added Taxon type and properties * Added Sample type * Added Study type * Change sample to sampleUsed * Added ranges to boundMolecule And fix "typo" on ranges for LabProtocol sampleUsed * Move Protein properties to BioChemEntity * Added definitions for types: BioChemEntity, ChemicalSubstance, MolecularEntity, and Protein * Initial DataRecord definition Included one class and one property that need to be updated * DataRecord class description * Initial course properties @njall to complete * included in dataset property * datasource removed - not sure what this does * Update protein and proteinstructure types * Update Protein description * Rename ProteinStructure to BioChemStructure * Add BioChemStructure description * Fix typo on massResolution BioChemStructure property * Update text for boundMolecule property in BioChemStructure * Update creationMethod property description to include not only annotation but also BioChemEntity * Update sequenceLocation property description to include not only annotation but also BioChemEntity * Add one initial example to BioChemEntity * Update bio.rdfa * initial example * Use always DefinedTerm rather than CategoryCode Note: Terms in an ontology are not necessarily categorical so DefinedTerm is a safer option * uniprot record example * Add URL to expected type for GO related properties * @njall is going to do this directly on schema.org This file is no longer needed. * Fix to make DataRecord work on appspot Means that appspot no longer gives a 500 error * Improve metadata on DataRecord Using the example of metadata capture from Course extension as good practice here * Redefining Sample as BioSample * Added collector property to BioSample * Added custodiam property * Added dateCreated property to BioSample * Added location properties to BioSample * Added material property to BioSample * Created age property on BioSample * Created phenotype property on BioSample * Added gender to BioSample * Made note that we need a definition for phenotype * created pedigree property on BioSample * Created isControl property on BioSample * Updating schema.org code to latest version * Extracted Gene definition from main file * Fixed definition of inverse properties * Gene definition fixes BioSchemas/specifications#272 * Removed hasOrtholog property fixes BioSchemas/specifications#276 * Removed hasHomolog property Fixes BioSchemas/specifications#275 * expressedIn definition added Issue BioSchemas/specifications#274 * Removed affectsFunction property Fixes BioSchemas/specifications#273 * Removed presentInCollection property from Gene BioSchemas/specifications#278 * Removed partOfOperon property Fixes issue BioSchemas/specifications#277 * Added link to GitHub issue to track reviews * Fixed data record example so that it displays * Rename age property to samplingAge Discussed in issue BioSchemas/specifications#306 * Removed old comment * Updated location properties As per discussion in issue BioSchemas/specifications#306 * Removed material property from Biosample As per discussion on mailing list and captured in issue BioSchemas/specifications#306 * Removing pedigree property from BioSample As per discussion in issue BioSchemas/specifications#306 * phenotype property removed from BioSample No clear indication of the usage currently, as discussed in issues BioSchemas/specifications#306 and BioSchemas/specifications#319 * Separated each type into its own file * Corrected typo in SequenceAnnotation * Move isEncodedByBCE and inverse to BioChemEntity * Hiding types that will not be included in the first release * Hiding ranges where types not part of delivery. * Removed hasSequenceAnnotation property from BioChemEntity * Only link to types that are included in the release * Notes on the derivation of BioSample * Fixed formatting * Summary of design decisions * Summary of design decisions * Missed smiles property * Added ToDo task * Removed text that is only pertinent to BioSample * Summary of design decisions * Summary of design decisions * Summary of design decisions * Summary of design decisions * Updated defn BioSchemas/specifications#327 * Added chemicalComposition BioSchemas/specifications#327 * Correct property definitions BioSchemas/specifications#327 * Added details of ontologies used in design * adding issues and mailing list to BCE * updating mailing list links * correcting whitespace issue * Refined text for links to issues and discussions * changing issue to issues * Refined text for links to issues and discussions * fixing typo * Refined text for links to issues and discussions * fixing typo * Refined text for links to issues and discussions * fixing typo * Refined text for links to issues and discussions * Refined text for links to issues and discussions * Refined text for links to issues and discussions * Two minor tweaks in the description. - IUPAC names are not only for organic compounds - the InChI is mostly for molecular entities and captures the chemical graph largely (and not chemical substances in general) * Restored 'molecular weight as Text' Closes BioSchemas/specifications#347 * Added statement to track issue * Updated to also allow QuantitativeValue. * Updated the `Number` example with representative examples for molecular weight. * Added links to issues, corrected labels of links * Fixed links to related issues * Started drafting readme file * Renamed file for consistency * Drafted release notes * Removed completed ToDos. Reformatted presentation of properties * Added note about schema:Substance. Closes BioSchemas/specifications#327 * Added relationship to domain ontologies, closes BioSchemas/specifications#348 * Fixed display issues * taxonRank is not equivalent but based on dwc:taxonRank dwc:taxonRank takes only literal values whereas the new taxonRank property may take literals as well as URIs from third party vocabularies * Declare hasSequence as a subPropertyOf hasRepresentation * Renamed hasSequence and updated definition * Declare sub-property relationships for MolecularEntity properties * Clarified smiles representations * Converted BioChemEntity to turtle representation * Converted to turtle * Converted to turtle * Converted to turtle * Converted to turtle * Converted to turtle * Converted to turtle * Moved coding notes to Bioschemas/specifications repo * Updated links to coding notes * Updated description of deployments * Removed files for types not being submitted These files are all available on BioChemEntity branch * Removed BioSample from first submission * Tweaks to pass tests and remove not needed old files * Actions issue #2862 - introduce Bioschema terms into pending * Fixed typo Co-authored-by: ljgarcia <leylajael@gmail.com> Co-authored-by: Alasdair Gray <A.J.G.Gray@hw.ac.uk> Co-authored-by: ljgc <ljgarcia@users.noreply.github.com> Co-authored-by: Sarala M. Wimalaratne <sarala.dissanayake@gmail.com> Co-authored-by: Kenneth McLeod <kcm1@hw.ac.uk> Co-authored-by: Egon Willighagen <egon.willighagen@gmail.com> Co-authored-by: Franck Michel <frmichel@users.noreply.github.com> Co-authored-by: Dataliberate <rjw@dataliberate.com>
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This is to introduce the terms from PR #2711 "Core Types to Support the Discovery of Life Sciences Resources". That PR introduced a new 'bio' area to contain term definitions.
This issue follows the current practice of introducing the new terms into the pending area
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