Update DRAO with latest versions of incorporated ontologies.

[allysonlister]

Before we start updating DRAO, we need to update the member ontologies and ensure there are no resulting conflicts. This ticket covers that update.

[allysonlister]

Ontofox was run to regenerate the external ontology terms and their hierarchies. The following is the markdown of the resulting Robot diff

Ontology comparison

Left

• Ontology IRI: http://www.fairsharing.org/ontology/domain/DRAO.owl
• Version IRI: None
• Loaded from: /domain-ontology/development/DRAO-merged.owl

Right

• Ontology IRI: http://www.fairsharing.org/ontology/domain/DRAO.owl
• Version IRI: None
• Loaded from: /domain-ontology/development/build/DRAO-merged.owl

Ontology imports

Ontology annotations

ATC code http://edamontology.org/data_3103

Removed

• ATC code SubClassOf Drug accession

Added

• ATC code SubClassOf Accession

• ATC code SubClassOf Drug identifier

Biological imaging http://edamontology.org/topic_3383

Removed

• Biological imaging label "Biological imaging"

Added

• Biological imaging 替代术语 "Biological imaging"

• Biological imaging label "Bioimaging"

Chemical structure image http://edamontology.org/data_1712

Added

• Chemical structure image 替代术语 "Small molecule sketch"

• Chemical structure image 替代术语 "Chemical structure sketch"

Compound identifier http://edamontology.org/data_1086

Added

• Compound identifier 替代术语 "Compound ID"

Data acquisition http://edamontology.org/topic_3077

Added

• Data acquisition 替代术语 "Data collection"

Data retrieval http://edamontology.org/operation_2422

Added

• Data retrieval 替代术语 "Data extraction"

• Data retrieval SubClassOf Text mining

DeprecatedClass http://www.w3.org/2002/07/owl#DeprecatedClass

Added

• DeprecatedClass imported from EDAM.owl

• Class: DeprecatedClass

Drug accession http://edamontology.org/data_2895

Removed

• Drug accession imported from EDAM.owl

• Drug accession label "Drug accession"

• Drug accession definition "Accession of a drug."

• Class: Drug accession

• Drug accession SubClassOf Drug identifier

• Drug accession SubClassOf Accession

Drug report http://edamontology.org/data_1696

Removed

• Drug report definition "An informative report on a specific drug."

Added

• Drug report definition "A human-readable collection of information about a specific drug."

• Drug report 替代术语 "Drug structure relationship map"

EC number http://edamontology.org/data_1011

Added

• EC number SubClassOf Accession

Evidence http://edamontology.org/data_2042

Removed

• Evidence definition "Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc."

Added

• Evidence definition "Typically a human-readable summary of body of facts or information indicating why a statement is true or valid. This may include a computational prediction, laboratory experiment, literature reference etc."

Experiment report http://edamontology.org/data_2531

Removed

• Experiment report label "Experiment report"

• Experiment report definition "Annotation on a wet lab experiment, such as experimental conditions."

Added

• Experiment report label "Protocol"

• Experiment report definition "A human-readable collection of information about about how a scientific experiment or analysis was carried out that results in a specific set of data or results used for further analysis or to test a specific hypothesis."

• Experiment report 替代术语 "Experiment report"

GO-term enrichment report http://edamontology.org/data_3754

Removed

• GO-term enrichment report label "GO-term enrichment report"

• GO-term enrichment report definition "An informative report containing a ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins."

• GO-term enrichment report SubClassOf Report

Added

• GO-term enrichment report 替代术语 "GO-term enrichment report"

• GO-term enrichment report label "GO-term enrichment data"

• GO-term enrichment report definition "A ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins."

• GO-term enrichment report SubClassOf Data

Gene expression data http://edamontology.org/data_2603

Removed

• Gene expression data definition "Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification."

• Gene expression data label "Gene expression data"

Added

• Gene expression data 替代术语 "Gene expression data"

• Gene expression data 替代术语 "Metabolite expression data"

• Gene expression data definition "Image, hybridisation or some other data arising from a study of feature/molecule expression, typically profiling or quantification."

• Gene expression data label "Expression data"

• Gene expression data 替代术语 "Protein expression data"

Gene prediction http://edamontology.org/operation_2454

Removed

• Gene prediction definition "Detect, predict and identify genes or components of genes in DNA sequences, including promoters, coding regions, splice sites, etc. "

• Gene prediction SubClassOf Nucleic acid feature detection

Added

• Gene prediction definition "Detect, predict and identify genes or components of genes in DNA sequences, including promoters, coding regions, splice sites, etc."

• Gene prediction SubClassOf Nucleic acid sequence analysis

Genome alignment http://edamontology.org/operation_3182

Added

• Genome alignment SubClassOf operation_3918

Genome annotation http://edamontology.org/operation_0362

Added

• Genome annotation 替代术语 "Functional genome annotation"

• Genome annotation 替代术语 "Structural genome annotation"

• Genome annotation SubClassOf operation_3918

Genome assembly http://edamontology.org/operation_0525

Removed

• Genome assembly SubClassOf Sequence assembly

Added

• Genome assembly SubClassOf Nucleic acid sequence analysis

• Genome assembly SubClassOf operation_3918

Genome visualisation http://edamontology.org/operation_3208

Added

• Genome visualisation SubClassOf operation_3918

Hidden Markov model http://edamontology.org/data_1364

Removed

• Hidden Markov model SubClassOf Sequence signature data

IAO_0020000 http://purl.obolibrary.org/obo/IAO_0020000

Added

• IAO_0020000 imported from iao.owl

• IAO_0020000 definition "An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity."@en

• IAO_0020000 label "identifier"@en

• Class: IAO_0020000

• IAO_0020000 SubClassOf information content entity

Identifier (typed) http://edamontology.org/data_0976

Removed

• Identifier (typed) label "Identifier (typed)"

Added

• Identifier (typed) 替代术语 "Identifier (typed)"

• Identifier (typed) label "Identifier (by type of data)"

Laboratory animal science http://edamontology.org/topic_3386

Added

• Laboratory animal science 替代术语 "Animal testing"

• Laboratory animal science 替代术语 "Animal experimentation"

• Laboratory animal science 替代术语 "Animal research"

• Laboratory animal science 替代术语 "In vivo testing"

Mass spectrometry spectra http://edamontology.org/data_0943

Removed

• Mass spectrometry spectra label "Mass spectrometry spectra"

Added

• Mass spectrometry spectra 替代术语 "Mass spectrometry spectra"

• Mass spectrometry spectra label "Mass spectrum"

Medical imaging http://edamontology.org/topic_3384

Added

• Medical imaging 替代术语 "Neuroimaging"

Molecule accession http://edamontology.org/data_2901

Removed

• Molecule accession imported from EDAM.owl

• Molecule accession definition "Accession of a specific molecule (catalogued in a database)."

• Molecule accession label "Molecule accession"

• Class: Molecule accession

• Molecule accession SubClassOf Molecule identifier

• Molecule accession SubClassOf Accession

Network simulation http://edamontology.org/operation_3562

Removed

• Network simulation 替代术语 "Pathway simulation"

• Network simulation 替代术语 "Network topology simulation"

• Network simulation SubClassOf Operation

Added

• Network simulation SubClassOf DeprecatedClass

Nucleic acid design http://edamontology.org/operation_3095

Added

• Nucleic acid design 替代术语 "Gene design"

Nucleic acid feature detection http://edamontology.org/operation_0415

Removed

• Nucleic acid feature detection 替代术语 "Sequence feature detection (nucleic acid)"

• Nucleic acid feature detection 替代术语 "Nucleic acid site detection"

• Nucleic acid feature detection 替代术语 "Nucleic acid site recognition"

• Nucleic acid feature detection imported from EDAM.owl

• Nucleic acid feature detection 替代术语 "Nucleic acid feature prediction"

• Nucleic acid feature detection 替代术语 "Nucleic acid site prediction"

• Nucleic acid feature detection 替代术语 "Nucleic acid feature recognition"

• Nucleic acid feature detection label "Nucleic acid feature detection"

• Nucleic acid feature detection definition "Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions."

• Class: Nucleic acid feature detection

• Nucleic acid feature detection SubClassOf Nucleic acid sequence analysis

• Nucleic acid feature detection SubClassOf Prediction and recognition

Nucleic acid property http://edamontology.org/data_0912

Added

• Nucleic acid property 替代术语 "Nucleic acid structural property"

• Nucleic acid property 替代术语 "Nucleic acid property (structural)"

OBI_0001177 http://purl.obolibrary.org/obo/OBI_0001177

Added

• OBI_0001177 imported from obi.owl

• OBI_0001177 definition "An assay that determines the sequence of an RNA molecule."

• OBI_0001177 label "RNA sequencing assay"

• Class: OBI_0001177

• OBI_0001177 SubClassOf sequencing assay

Pathway or network prediction http://edamontology.org/operation_3439

Removed

• Pathway or network prediction 替代术语 "Network prediction"

• Pathway or network prediction 替代术语 "Pathway prediction"

• Pathway or network prediction 替代术语 "Protein interaction network prediction"

• Pathway or network prediction 替代术语 "Gene regulatory network prediction"

• Pathway or network prediction SubClassOf Analysis

• Pathway or network prediction SubClassOf Prediction and recognition

Added

• Pathway or network prediction SubClassOf DeprecatedClass

Post-translation modification site prediction http://edamontology.org/operation_0417

Removed

• Post-translation modification site prediction label "Post-translation modification site prediction"

• Post-translation modification site prediction 替代术语 "PTM site prediction"

Added

• Post-translation modification site prediction label "PTM site prediction"

• Post-translation modification site prediction 替代术语 "Post-translation modification site prediction"

• Post-translation modification site prediction 替代术语 "Post-translational modification analysis"

• Post-translation modification site prediction 替代术语 "Post-translational modification site prediction"

Protein accession http://edamontology.org/data_2907

Removed

• Protein accession SubClassOf Molecule accession

Added

• Protein accession SubClassOf Molecule identifier

Protein binding site prediction http://edamontology.org/operation_2575

Removed

• Protein binding site prediction 替代术语 " Active site prediction"

• Protein binding site prediction 替代术语 "Binding site prediction"

• Protein binding site prediction label "Protein binding site prediction"

• Protein binding site prediction 替代术语 "Ligand-binding site prediction"

• Protein binding site prediction SubClassOf Protein interaction prediction

Added

• Protein binding site prediction 替代术语 "Protein binding site prediction"

• Protein binding site prediction label "Binding site prediction"

• Protein binding site prediction SubClassOf Protein function prediction

Protein circular dichroism (CD) spectroscopic data http://edamontology.org/data_0939

Removed

• Protein circular dichroism (CD) spectroscopic data label "Protein circular dichroism (CD) spectroscopic data"

Added

• Protein circular dichroism (CD) spectroscopic data 替代术语 "CD spectrum"

• Protein circular dichroism (CD) spectroscopic data 替代术语 "Protein circular dichroism (CD) spectroscopic data"

• Protein circular dichroism (CD) spectroscopic data label "CD spectra"

Protein function analysis http://edamontology.org/operation_2414

Removed

• Protein function analysis definition "Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report."

• Protein function analysis label "Protein function analysis"

• Protein function analysis imported from EDAM.owl

• Class: Protein function analysis

• Protein function analysis SubClassOf Analysis

Protein function prediction http://edamontology.org/operation_1777

Removed

• Protein function prediction definition "Predict general functional properties of a protein."

• Protein function prediction SubClassOf Protein function analysis

Added

• Protein function prediction 替代术语 "Protein functional analysis"

• Protein function prediction 替代术语 "Protein function analysis"

• Protein function prediction definition "Predict the biological or biochemical role of a protein, or other aspects of a protein function."

• Protein function prediction SubClassOf Analysis

Protein interaction prediction http://edamontology.org/operation_2492

Removed

• Protein interaction prediction definition "Predict the interactions of proteins with other molecules."

• Protein interaction prediction SubClassOf Protein function analysis

Added

• Protein interaction prediction 替代术语 "Protein-protein interaction prediction"

• Protein interaction prediction 替代术语 "Protein-protein binding prediction"

• Protein interaction prediction definition "Predict the interactions of proteins with other proteins."

• Protein interaction prediction 替代术语 "Protein-protein interaction detection"

Protein interactions http://edamontology.org/topic_0128

Added

• Protein interactions 替代术语 "Protein interaction map"

• Protein interactions 替代术语 "Protein-RNA interactions"

• Protein interactions 替代术语 "Protein interactome"

• Protein interactions 替代术语 "Protein-DNA interactions"

Protein structure http://edamontology.org/data_1460

Removed

• Protein structure definition "3D coordinate and associated data for a protein tertiary (3D) structure."

Added

• Protein structure definition "3D coordinate and associated data for a protein tertiary (3D) structure, or part of a structure, possibly in complex with other molecules."

RNA-seq assay http://purl.obolibrary.org/obo/OBI_0001271

Removed

• RNA-seq assay definition "An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance."

• RNA-seq assay SubClassOf sequencing assay

• RNA-seq assay SubClassOf transcription profiling assay

Added

• RNA-seq assay definition "An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance."

• RNA-seq assay SubClassOf OBI_0001177

Report http://edamontology.org/data_2048

Added

• Report 替代术语 "Record"

Sequence alignment (nucleic acid) http://edamontology.org/data_1383

Removed

• Sequence alignment (nucleic acid) label "Sequence alignment (nucleic acid)"

Added

• Sequence alignment (nucleic acid) label "Nucleic acid sequence alignment"

• Sequence alignment (nucleic acid) 替代术语 "DNA sequence alignment"

• Sequence alignment (nucleic acid) 替代术语 "RNA sequence alignment"

• Sequence alignment (nucleic acid) 替代术语 "Sequence alignment (nucleic acid)"

Sequence assembly http://edamontology.org/operation_0310

Removed

• Sequence assembly definition "Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence."

• Sequence assembly label "Sequence assembly"

• Sequence assembly 替代术语 "Sequence assembly editing"

• Sequence assembly 替代术语 "Metagenomic assembly"

• Sequence assembly imported from EDAM.owl

• Class: Sequence assembly

• Sequence assembly SubClassOf Sequence analysis

• Sequence assembly SubClassOf Nucleic acid sequence analysis

Sequence motif http://edamontology.org/data_1353

Removed

• Sequence motif SubClassOf Sequence signature data

Added

• Sequence motif SubClassOf Data

Sequence set http://edamontology.org/data_0850

Removed

• Sequence set definition "A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method."

Added

• Sequence set definition "A collection of one or typically multiple molecular sequences (which can include derived data or metadata) that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method."

• Sequence set 替代术语 "Alignment reference"

Sequence signature data http://edamontology.org/data_0860

Removed

• Sequence signature data imported from EDAM.owl

• Sequence signature data definition "Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element."

• Sequence signature data label "Sequence signature data"

• Class: Sequence signature data

• Sequence signature data SubClassOf Data

centrally registered identifier http://purl.obolibrary.org/obo/IAO_0000578

Removed

• centrally registered identifier SubClassOf information content entity

Added

• centrally registered identifier SubClassOf IAO_0020000

cytometry assay http://purl.obolibrary.org/obo/OBI_0001977

Removed

• cytometry assay definition "An assay that measures properties of cells."

Added

• cytometry assay definition "An assay that counts and/or measures characteristics of cells."

embryonic cell http://purl.obolibrary.org/obo/CL_0002321

Removed

• embryonic cell label "embryonic cell"

Added

• embryonic cell label "embryonic cell (metazoa)"

enzymatic cleavage http://purl.obolibrary.org/obo/OBI_0000231

Removed

• enzymatic cleavage definition "enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme"@en

Added

• enzymatic cleavage definition "a material processing that digests the fraction of input material that is susceptible to that enzyme"@en

food http://purl.obolibrary.org/obo/CHEBI_33290

Removed

• food definition "Any material that can be ingested by an organism."

Added

• food definition "A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life."

genetic disorder http://www.ebi.ac.uk/efo/EFO_0000508

Added

• genetic disorder 替代术语 "Mendelian disease"

genetic modification http://www.ebi.ac.uk/efo/EFO_0000510

Removed

• genetic modification SubClassOf experimental process

Added

• genetic modification SubClassOf process

intracellular http://purl.obolibrary.org/obo/GO_0005622

Removed

• intracellular label "intracellular"

• intracellular definition "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm."

• intracellular SubClassOf cellular_component

Added

• intracellular definition "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm."

• intracellular 替代术语 "intracellular"

• intracellular label "intracellular anatomical structure"

• intracellular SubClassOf cellular anatomical entity

intracellular organelle http://purl.obolibrary.org/obo/GO_0043229

Removed

• intracellular organelle SubClassOf organelle

Added

• intracellular organelle SubClassOf intracellular

journal article http://purl.obolibrary.org/obo/IAO_0000013

Added

• journal article SubClassOf publication

meiotic nuclear division http://purl.obolibrary.org/obo/GO_0140013

Added

• meiotic nuclear division 替代术语 "meiosis"

obsolete cell http://purl.obolibrary.org/obo/GO_0005623

Removed

• obsolete cell imported from cl.owl

• obsolete cell label "cell"

• obsolete cell definition "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope."

• obsolete cell SubClassOf anatomical structure

operation_3918 http://edamontology.org/operation_3918

Added

• operation_3918 label "Genome analysis"

• operation_3918 definition "Detects chimeric sequences (chimeras) from a sequence alignment."

• operation_3918 imported from EDAM.owl

• Class: operation_3918

• operation_3918 SubClassOf Nucleic acid sequence analysis

operon http://purl.obolibrary.org/obo/SO_0000178

Removed

• operon definition "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region."

Added

• operon definition "The DNA region of a group of adjacent genes whose transcription is coordinated on one or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene."

process http://purl.obolibrary.org/obo/BFO_0000015

Added

• process definition "A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs."

• process imported from efo.owl

• process SubClassOf Thing

promoter http://purl.obolibrary.org/obo/SO_0000167

Removed

• promoter definition "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery."

Added

• promoter definition "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription."

protein http://purl.obolibrary.org/obo/PR_000000001

Added

• protein 替代术语 "natural protein"

• protein 替代术语 "native protein"

publication http://purl.obolibrary.org/obo/IAO_0000311

Removed

• publication definition "A document that has been accepted by a publisher"@en

Added

• publication definition "A document that is the output of a publishing process."@en

treatment http://www.ebi.ac.uk/efo/EFO_0000727

Removed

• treatment definition "A process in which the act is intended to modify or alter some other material entity,"

• treatment SubClassOf experimental process

Added

• treatment definition "A planned process intended to modify or alter a condition or characteristic of an organism or individual."

• treatment SubClassOf process

[allysonlister]

http://edamontology.org/operation_3562 (Network simulation) is now obsolete in EDAM.

[allysonlister]

http://edamontology.org/operation_3439 (Pathway or network prediction) is now obsolete in EDAM.

[allysonlister]

http://purl.obolibrary.org/obo/GO_0005623 (Obsolete cell) needs to be checked and possibly refactored.

[allysonlister]

Have updated DRAO to remove & replace all deprecated terms. Here's the updated diff file:

Ontology comparison

Left

• Ontology IRI: http://www.fairsharing.org/ontology/domain/DRAO.owl
• Version IRI: None
• Loaded from: file:/development/DRAO-merged.owl

Right

• Ontology IRI: http://www.fairsharing.org/ontology/domain/DRAO.owl
• Version IRI: None
• Loaded from: file:development/build/DRAO-merged.owl

Ontology imports

Ontology annotations

ATC code http://edamontology.org/data_3103

Removed

• ATC code SubClassOf Drug accession

Added

• ATC code SubClassOf Accession

• ATC code SubClassOf Drug identifier

Biological imaging http://edamontology.org/topic_3383

Removed

• Biological imaging label "Biological imaging"

Added

• Biological imaging 替代术语 "Biological imaging"

• Biological imaging label "Bioimaging"

CL_0000000 http://purl.obolibrary.org/obo/CL_0000000

Added

• CL_0000000 inSubset "FAIRsharing"@en

• CL_0000000 definition "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane."

• CL_0000000 FAIRsharing alternative term "Cell"@en

• CL_0000000 label "cell"

• CL_0000000 label "cell"@en

• CL_0000000 imported from cl.owl

• Class: CL_0000000

• CL_0000000 SubClassOf anatomical structure

CL_0000211 http://purl.obolibrary.org/obo/CL_0000211

Added

• CL_0000211 label "electrically active cell"

• CL_0000211 definition "A cell whose function is determined by the generation or the reception of an electric signal."

• CL_0000211 imported from cl.owl

• Class: CL_0000211

• CL_0000211 SubClassOf native cell

CL_0000393 http://purl.obolibrary.org/obo/CL_0000393

Added

• CL_0000393 label "electrically responsive cell"

• CL_0000393 definition "A cell whose function is determined by its response to an electric signal."

• CL_0000393 imported from cl.owl

• Class: CL_0000393

• CL_0000393 SubClassOf CL_0000211

CL_0000404 http://purl.obolibrary.org/obo/CL_0000404

Added

• CL_0000404 imported from cl.owl

• CL_0000404 definition "A cell that initiates an electrical signal and passes that signal to another cell."

• CL_0000404 label "electrically signaling cell"

• Class: CL_0000404

• CL_0000404 SubClassOf CL_0000211

CL_0002319 http://purl.obolibrary.org/obo/CL_0002319

Added

• CL_0002319 label "neural cell"

• CL_0002319 definition "A cell that is part of the nervous system."

• CL_0002319 imported from cl.owl

• Class: CL_0002319

• CL_0002319 SubClassOf somatic cell

• CL_0002319 SubClassOf animal cell

Chemical structure image http://edamontology.org/data_1712

Added

• Chemical structure image 替代术语 "Small molecule sketch"

• Chemical structure image 替代术语 "Chemical structure sketch"

Compound identifier http://edamontology.org/data_1086

Added

• Compound identifier 替代术语 "Compound ID"

Data acquisition http://edamontology.org/topic_3077

Added

• Data acquisition 替代术语 "Data collection"

Data retrieval http://edamontology.org/operation_2422

Added

• Data retrieval 替代术语 "Data extraction"

• Data retrieval SubClassOf Text mining

Drug accession http://edamontology.org/data_2895

Removed

• Drug accession imported from EDAM.owl

• Drug accession label "Drug accession"

• Drug accession definition "Accession of a drug."

• Class: Drug accession

• Drug accession SubClassOf Drug identifier

• Drug accession SubClassOf Accession

Drug report http://edamontology.org/data_1696

Removed

• Drug report definition "An informative report on a specific drug."

Added

• Drug report definition "A human-readable collection of information about a specific drug."

• Drug report 替代术语 "Drug structure relationship map"

EC number http://edamontology.org/data_1011

Added

• EC number SubClassOf Accession

Evidence http://edamontology.org/data_2042

Removed

• Evidence definition "Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc."

Added

• Evidence definition "Typically a human-readable summary of body of facts or information indicating why a statement is true or valid. This may include a computational prediction, laboratory experiment, literature reference etc."

Experiment report http://edamontology.org/data_2531

Removed

• Experiment report label "Experiment report"

• Experiment report definition "Annotation on a wet lab experiment, such as experimental conditions."

Added

• Experiment report label "Protocol"

• Experiment report definition "A human-readable collection of information about about how a scientific experiment or analysis was carried out that results in a specific set of data or results used for further analysis or to test a specific hypothesis."

• Experiment report 替代术语 "Experiment report"

GO-term enrichment report http://edamontology.org/data_3754

Removed

• GO-term enrichment report label "GO-term enrichment report"

• GO-term enrichment report definition "An informative report containing a ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins."

• GO-term enrichment report SubClassOf Report

Added

• GO-term enrichment report 替代术语 "GO-term enrichment report"

• GO-term enrichment report label "GO-term enrichment data"

• GO-term enrichment report definition "A ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins."

• GO-term enrichment report SubClassOf Data

Gene expression data http://edamontology.org/data_2603

Removed

• Gene expression data definition "Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification."

• Gene expression data label "Gene expression data"

Added

• Gene expression data 替代术语 "Gene expression data"

• Gene expression data 替代术语 "Metabolite expression data"

• Gene expression data definition "Image, hybridisation or some other data arising from a study of feature/molecule expression, typically profiling or quantification."

• Gene expression data label "Expression data"

• Gene expression data 替代术语 "Protein expression data"

Gene prediction http://edamontology.org/operation_2454

Removed

• Gene prediction definition "Detect, predict and identify genes or components of genes in DNA sequences, including promoters, coding regions, splice sites, etc. "

• Gene prediction SubClassOf Nucleic acid feature detection

Added

• Gene prediction definition "Detect, predict and identify genes or components of genes in DNA sequences, including promoters, coding regions, splice sites, etc."

• Gene prediction SubClassOf Nucleic acid sequence analysis

Genome alignment http://edamontology.org/operation_3182

Added

• Genome alignment SubClassOf operation_3918

Genome annotation http://edamontology.org/operation_0362

Added

• Genome annotation 替代术语 "Functional genome annotation"

• Genome annotation 替代术语 "Structural genome annotation"

• Genome annotation SubClassOf operation_3918

Genome assembly http://edamontology.org/operation_0525

Removed

• Genome assembly SubClassOf Sequence assembly

Added

• Genome assembly SubClassOf Nucleic acid sequence analysis

• Genome assembly SubClassOf operation_3918

Genome visualisation http://edamontology.org/operation_3208

Added

• Genome visualisation SubClassOf operation_3918

Hidden Markov model http://edamontology.org/data_1364

Removed

• Hidden Markov model SubClassOf Sequence signature data

IAO_0020000 http://purl.obolibrary.org/obo/IAO_0020000

Added

• IAO_0020000 imported from iao.owl

• IAO_0020000 definition "An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity."@en

• IAO_0020000 label "identifier"@en

• Class: IAO_0020000

• IAO_0020000 SubClassOf information content entity

Identifier (typed) http://edamontology.org/data_0976

Removed

• Identifier (typed) label "Identifier (typed)"

Added

• Identifier (typed) 替代术语 "Identifier (typed)"

• Identifier (typed) label "Identifier (by type of data)"

Laboratory animal science http://edamontology.org/topic_3386

Added

• Laboratory animal science 替代术语 "Animal testing"

• Laboratory animal science 替代术语 "Animal experimentation"

• Laboratory animal science 替代术语 "Animal research"

• Laboratory animal science 替代术语 "In vivo testing"

Mass spectrometry spectra http://edamontology.org/data_0943

Removed

• Mass spectrometry spectra label "Mass spectrometry spectra"

Added

• Mass spectrometry spectra 替代术语 "Mass spectrometry spectra"

• Mass spectrometry spectra label "Mass spectrum"

Medical imaging http://edamontology.org/topic_3384

Added

• Medical imaging 替代术语 "Neuroimaging"

Molecule accession http://edamontology.org/data_2901

Removed

• Molecule accession imported from EDAM.owl

• Molecule accession definition "Accession of a specific molecule (catalogued in a database)."

• Molecule accession label "Molecule accession"

• Class: Molecule accession

• Molecule accession SubClassOf Molecule identifier

• Molecule accession SubClassOf Accession

Network simulation http://edamontology.org/operation_3562

Removed

• Network simulation 替代术语 "Pathway simulation"

• Network simulation inSubset "FAIRsharing"@en

• Network simulation 替代术语 "Network topology simulation"

• Network simulation definition "Simulate the bevaviour of a biological pathway or network."

• Network simulation label "Network simulation"

• Network simulation imported from EDAM.owl

• Class: Network simulation

• Network simulation SubClassOf Operation

Nucleic acid design http://edamontology.org/operation_3095

Added

• Nucleic acid design 替代术语 "Gene design"

Nucleic acid feature detection http://edamontology.org/operation_0415

Removed

• Nucleic acid feature detection 替代术语 "Sequence feature detection (nucleic acid)"

• Nucleic acid feature detection 替代术语 "Nucleic acid site detection"

• Nucleic acid feature detection 替代术语 "Nucleic acid site recognition"

• Nucleic acid feature detection imported from EDAM.owl

• Nucleic acid feature detection 替代术语 "Nucleic acid feature prediction"

• Nucleic acid feature detection 替代术语 "Nucleic acid site prediction"

• Nucleic acid feature detection 替代术语 "Nucleic acid feature recognition"

• Nucleic acid feature detection label "Nucleic acid feature detection"

• Nucleic acid feature detection definition "Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions."

• Class: Nucleic acid feature detection

• Nucleic acid feature detection SubClassOf Nucleic acid sequence analysis

• Nucleic acid feature detection SubClassOf Prediction and recognition

Nucleic acid property http://edamontology.org/data_0912

Added

• Nucleic acid property 替代术语 "Nucleic acid structural property"

• Nucleic acid property 替代术语 "Nucleic acid property (structural)"

OBI_0001177 http://purl.obolibrary.org/obo/OBI_0001177

Added

• OBI_0001177 imported from obi.owl

• OBI_0001177 definition "An assay that determines the sequence of an RNA molecule."

• OBI_0001177 label "RNA sequencing assay"

• Class: OBI_0001177

• OBI_0001177 SubClassOf sequencing assay

Pathway or network prediction http://edamontology.org/operation_3439

Removed

• Pathway or network prediction 替代术语 "Network prediction"

• Pathway or network prediction definition "Predict a molecular pathway or network."

• Pathway or network prediction 替代术语 "Pathway prediction"

• Pathway or network prediction imported from EDAM.owl

• Pathway or network prediction inSubset "FAIRsharing"@en

• Pathway or network prediction 替代术语 "Protein interaction network prediction"

• Pathway or network prediction 替代术语 "Gene regulatory network prediction"

• Pathway or network prediction label "Pathway or network prediction"

• Class: Pathway or network prediction

• Pathway or network prediction SubClassOf Analysis

• Pathway or network prediction SubClassOf Prediction and recognition

Post-translation modification site prediction http://edamontology.org/operation_0417

Removed

• Post-translation modification site prediction label "Post-translation modification site prediction"

• Post-translation modification site prediction 替代术语 "PTM site prediction"

Added

• Post-translation modification site prediction label "PTM site prediction"

• Post-translation modification site prediction 替代术语 "Post-translation modification site prediction"

• Post-translation modification site prediction 替代术语 "Post-translational modification analysis"

• Post-translation modification site prediction 替代术语 "Post-translational modification site prediction"

Prediction and recognition http://edamontology.org/operation_2423

Removed

• Prediction and recognition FAIRsharing alternative term "Computational predictions"@en

Added

• Prediction and recognition FAIRsharing alternative term "Computational biological predictions"@en

Protein accession http://edamontology.org/data_2907

Removed

• Protein accession SubClassOf Molecule accession

Added

• Protein accession SubClassOf Molecule identifier

Protein binding site prediction http://edamontology.org/operation_2575

Removed

• Protein binding site prediction 替代术语 " Active site prediction"

• Protein binding site prediction 替代术语 "Binding site prediction"

• Protein binding site prediction label "Protein binding site prediction"

• Protein binding site prediction 替代术语 "Ligand-binding site prediction"

• Protein binding site prediction SubClassOf Protein interaction prediction

Added

• Protein binding site prediction 替代术语 "Protein binding site prediction"

• Protein binding site prediction label "Binding site prediction"

• Protein binding site prediction SubClassOf Protein function prediction

Protein circular dichroism (CD) spectroscopic data http://edamontology.org/data_0939

Removed

• Protein circular dichroism (CD) spectroscopic data label "Protein circular dichroism (CD) spectroscopic data"

Added

• Protein circular dichroism (CD) spectroscopic data 替代术语 "CD spectrum"

• Protein circular dichroism (CD) spectroscopic data 替代术语 "Protein circular dichroism (CD) spectroscopic data"

• Protein circular dichroism (CD) spectroscopic data label "CD spectra"

Protein function analysis http://edamontology.org/operation_2414

Removed

• Protein function analysis definition "Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report."

• Protein function analysis label "Protein function analysis"

• Protein function analysis imported from EDAM.owl

• Class: Protein function analysis

• Protein function analysis SubClassOf Analysis

Protein function prediction http://edamontology.org/operation_1777

Removed

• Protein function prediction definition "Predict general functional properties of a protein."

• Protein function prediction SubClassOf Protein function analysis

Added

• Protein function prediction 替代术语 "Protein functional analysis"

• Protein function prediction 替代术语 "Protein function analysis"

• Protein function prediction definition "Predict the biological or biochemical role of a protein, or other aspects of a protein function."

• Protein function prediction SubClassOf Analysis

Protein interaction prediction http://edamontology.org/operation_2492

Removed

• Protein interaction prediction definition "Predict the interactions of proteins with other molecules."

• Protein interaction prediction SubClassOf Protein function analysis

Added

• Protein interaction prediction 替代术语 "Protein-protein interaction prediction"

• Protein interaction prediction 替代术语 "Protein-protein binding prediction"

• Protein interaction prediction definition "Predict the interactions of proteins with other proteins."

• Protein interaction prediction 替代术语 "Protein-protein interaction detection"

Protein interactions http://edamontology.org/topic_0128

Added

• Protein interactions 替代术语 "Protein interaction map"

• Protein interactions 替代术语 "Protein-RNA interactions"

• Protein interactions 替代术语 "Protein interactome"

• Protein interactions 替代术语 "Protein-DNA interactions"

Protein structure http://edamontology.org/data_1460

Removed

• Protein structure definition "3D coordinate and associated data for a protein tertiary (3D) structure."

Added

• Protein structure definition "3D coordinate and associated data for a protein tertiary (3D) structure, or part of a structure, possibly in complex with other molecules."

RNA-seq assay http://purl.obolibrary.org/obo/OBI_0001271

Removed

• RNA-seq assay definition "An transcription profiling assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance."

• RNA-seq assay SubClassOf sequencing assay

• RNA-seq assay SubClassOf transcription profiling assay

Added

• RNA-seq assay definition "An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance."

• RNA-seq assay SubClassOf OBI_0001177

Report http://edamontology.org/data_2048

Added

• Report 替代术语 "Record"

Sequence alignment (nucleic acid) http://edamontology.org/data_1383

Removed

• Sequence alignment (nucleic acid) label "Sequence alignment (nucleic acid)"

Added

• Sequence alignment (nucleic acid) label "Nucleic acid sequence alignment"

• Sequence alignment (nucleic acid) 替代术语 "DNA sequence alignment"

• Sequence alignment (nucleic acid) 替代术语 "RNA sequence alignment"

• Sequence alignment (nucleic acid) 替代术语 "Sequence alignment (nucleic acid)"

Sequence assembly http://edamontology.org/operation_0310

Removed

• Sequence assembly definition "Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence."

• Sequence assembly label "Sequence assembly"

• Sequence assembly 替代术语 "Sequence assembly editing"

• Sequence assembly 替代术语 "Metagenomic assembly"

• Sequence assembly imported from EDAM.owl

• Class: Sequence assembly

• Sequence assembly SubClassOf Sequence analysis

• Sequence assembly SubClassOf Nucleic acid sequence analysis

Sequence motif http://edamontology.org/data_1353

Removed

• Sequence motif SubClassOf Sequence signature data

Added

• Sequence motif SubClassOf Data

Sequence set http://edamontology.org/data_0850

Removed

• Sequence set definition "A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method."

Added

• Sequence set definition "A collection of one or typically multiple molecular sequences (which can include derived data or metadata) that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method."

• Sequence set 替代术语 "Alignment reference"

Sequence signature data http://edamontology.org/data_0860

Removed

• Sequence signature data imported from EDAM.owl

• Sequence signature data definition "Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element."

• Sequence signature data label "Sequence signature data"

• Class: Sequence signature data

• Sequence signature data SubClassOf Data

cell in vitro http://purl.obolibrary.org/obo/CL_0001034

Removed

• cell in vitro SubClassOf obsolete cell

Added

• cell in vitro SubClassOf CL_0000000

centrally registered identifier http://purl.obolibrary.org/obo/IAO_0000578

Removed

• centrally registered identifier SubClassOf information content entity

Added

• centrally registered identifier SubClassOf IAO_0020000

cytometry assay http://purl.obolibrary.org/obo/OBI_0001977

Removed

• cytometry assay definition "An assay that measures properties of cells."

Added

• cytometry assay definition "An assay that counts and/or measures characteristics of cells."

embryonic cell http://purl.obolibrary.org/obo/CL_0002321

Removed

• embryonic cell label "embryonic cell"

Added

• embryonic cell label "embryonic cell (metazoa)"

enzymatic cleavage http://purl.obolibrary.org/obo/OBI_0000231

Removed

• enzymatic cleavage definition "enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme"@en

Added

• enzymatic cleavage definition "a material processing that digests the fraction of input material that is susceptible to that enzyme"@en

food http://purl.obolibrary.org/obo/CHEBI_33290

Removed

• food definition "Any material that can be ingested by an organism."

Added

• food definition "A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life."

genetic disorder http://www.ebi.ac.uk/efo/EFO_0000508

Added

• genetic disorder 替代术语 "Mendelian disease"

genetic modification http://www.ebi.ac.uk/efo/EFO_0000510

Removed

• genetic modification SubClassOf experimental process

Added

• genetic modification SubClassOf process

intracellular http://purl.obolibrary.org/obo/GO_0005622

Removed

• intracellular label "intracellular"

• intracellular definition "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm."

• intracellular SubClassOf cellular_component

Added

• intracellular definition "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm."

• intracellular 替代术语 "intracellular"

• intracellular label "intracellular anatomical structure"

• intracellular SubClassOf cellular anatomical entity

intracellular organelle http://purl.obolibrary.org/obo/GO_0043229

Removed

• intracellular organelle SubClassOf organelle

Added

• intracellular organelle SubClassOf intracellular

journal article http://purl.obolibrary.org/obo/IAO_0000013

Added

• journal article SubClassOf publication

meiotic nuclear division http://purl.obolibrary.org/obo/GO_0140013

Added

• meiotic nuclear division 替代术语 "meiosis"

native cell http://purl.obolibrary.org/obo/CL_0000003

Removed

• native cell SubClassOf obsolete cell

Added

• native cell SubClassOf CL_0000000

neuron http://purl.obolibrary.org/obo/CL_0000540

Removed

• neuron SubClassOf obsolete cell

Added

• neuron SubClassOf CL_0000404

• neuron SubClassOf CL_0000393

• neuron SubClassOf CL_0002319

obsolete cell http://purl.obolibrary.org/obo/GO_0005623

Removed

• obsolete cell definition "OBSOLETE. The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope."

• obsolete cell inSubset "FAIRsharing"@en

• obsolete cell imported from go.owl

• obsolete cell imported from cl.owl

• obsolete cell label "obsolete cell"

• obsolete cell FAIRsharing alternative term "Cell"@en

• obsolete cell label "cell"

• obsolete cell definition "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope."

• Class: obsolete cell

• obsolete cell SubClassOf anatomical structure

operation_3918 http://edamontology.org/operation_3918

Added

• operation_3918 label "Genome analysis"

• operation_3918 definition "Detects chimeric sequences (chimeras) from a sequence alignment."

• operation_3918 imported from EDAM.owl

• Class: operation_3918

• operation_3918 SubClassOf Nucleic acid sequence analysis

operation_3927 http://edamontology.org/operation_3927

Added

• operation_3927 替代术语 "Biological network prediction"

• operation_3927 inSubset "FAIRsharing"@en

• operation_3927 imported from EDAM.owl

• operation_3927 替代术语 "Network comparison"

• operation_3927 label "Network analysis"

• operation_3927 替代术语 "Network modelling"

• operation_3927 替代术语 "Network simulation"

• operation_3927 definition "Generate, process or analyse a biological network."

• operation_3927 替代术语 "Network topology simulation"

• operation_3927 FAIRsharing alternative term "Biological network analysis"@en

• operation_3927 替代术语 "Biological network analysis"

• operation_3927 替代术语 "Network prediction"

• operation_3927 替代术语 "Biological network modelling"

• Class: operation_3927

• operation_3927 SubClassOf Analysis

operon http://purl.obolibrary.org/obo/SO_0000178

Removed

• operon definition "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region."

Added

• operon definition "The DNA region of a group of adjacent genes whose transcription is coordinated on one or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene."

process http://purl.obolibrary.org/obo/BFO_0000015

Added

• process definition "A process is an entity that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity during the time it occurs."

• process imported from efo.owl

• process SubClassOf Thing

promoter http://purl.obolibrary.org/obo/SO_0000167

Removed

• promoter definition "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery."

Added

• promoter definition "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription."

protein http://purl.obolibrary.org/obo/PR_000000001

Added

• protein 替代术语 "natural protein"

• protein 替代术语 "native protein"

publication http://purl.obolibrary.org/obo/IAO_0000311

Removed

• publication definition "A document that has been accepted by a publisher"@en

Added

• publication definition "A document that is the output of a publishing process."@en

treatment http://www.ebi.ac.uk/efo/EFO_0000727

Removed

• treatment definition "A process in which the act is intended to modify or alter some other material entity,"

• treatment SubClassOf experimental process

Added

• treatment definition "A planned process intended to modify or alter a condition or characteristic of an organism or individual."

• treatment SubClassOf process

unspecified cell type http://www.ebi.ac.uk/cellline#UnspecifiedCellType

Removed

• unspecified cell type SubClassOf obsolete cell

Added

• unspecified cell type SubClassOf CL_0000000

[allysonlister]

The outstanding question in #75 does not stop us moving forward with the other tickets in this milestone, therefore I am closing this ticket now that the DRAO external ontologies have been updated.