diff --git a/EDAM_dev.owl b/EDAM_dev.owl index a5225c7..b5f59d6 100644 --- a/EDAM_dev.owl +++ b/EDAM_dev.owl @@ -418,16 +418,16 @@ - true - In very unusual cases. + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. + OBO_REL:bearer_of - + - OBO_REL:bearer_of - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. + true + In very unusual cases. - + @@ -477,8 +477,8 @@ - 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. OBO_REL:has_participant + 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. @@ -505,17 +505,17 @@ - OBO_REL:has_participant - 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. - - - - true In very unusual cases. + + OBO_REL:has_participant + 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. + + + @@ -547,8 +547,8 @@ - true In very unusual cases. + true @@ -616,8 +616,8 @@ - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. OBO_REL:inheres_in + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. @@ -700,16 +700,16 @@ - In very unusual cases. - true + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. + OBO_REL:participates_in - + - OBO_REL:participates_in - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. + In very unusual cases. + true - + @@ -747,8 +747,8 @@ - In very unusual cases. true + In very unusual cases. @@ -806,8 +806,8 @@ - Data set EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Data set @@ -818,8 +818,8 @@ - Datum EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Datum @@ -5991,8 +5991,8 @@ - A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. UniProt|Enzyme Nomenclature + A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. @@ -6805,8 +6805,8 @@ beta12orEarlier http://purl.bioontology.org/ontology/MSH/D058977 SO:0000110 - This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. General sequence features + This includes annotation of positional sequence features, organised into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence. Features Feature record @@ -7023,9 +7023,9 @@ Feature table + Annotation of positional sequence features, organised into a standard feature table. Sequence feature table beta12orEarlier - Annotation of positional sequence features, organized into a standard feature table. @@ -9098,13 +9098,13 @@ - + - + beta12orEarlier @@ -10316,8 +10316,8 @@ Protein fold recognition report Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. + A report on known protein structural domains or folds that are recognised (identified) in protein sequence(s). beta12orEarlier - A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s). true beta12orEarlier @@ -10390,8 +10390,8 @@ Nucleic acid enthalpy + Enthalpy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). beta12orEarlier - Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). @@ -10403,7 +10403,7 @@ Nucleic acid entropy - Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + Entropy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). beta12orEarlier @@ -10416,7 +10416,7 @@ Nucleic acid melting temperature - Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + Melting temperature of hybridised or double stranded nucleic acid (DNA or RNA/DNA). beta12orEarlier beta12orEarlier true @@ -10431,8 +10431,8 @@ Nucleic acid stitch profile + Stitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA). beta12orEarlier - Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA). A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. @@ -14119,13 +14119,13 @@ - + - + Identifier of a codon usage table, for example a genetic code. @@ -14437,7 +14437,7 @@ Nucleic acid melting temperature beta12orEarlier - A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. + A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridised or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. Melting temperature @@ -15856,9 +15856,9 @@ Bit score - A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system. - Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. + Bit scores are normalised with respect to the scoring system and therefore can be used to compare alignment scores from different searches. beta12orEarlier + A score derived from the alignment of two sequences, which is then normalised with respect to the scoring system. @@ -18331,13 +18331,13 @@ - + - + beta12orEarlier @@ -20392,13 +20392,13 @@ - + - + Identifier of a lipid. @@ -23842,7 +23842,7 @@ Lane identifier - An identifier of a lane within a flow cell of a sequencing machine, within which millions of sequences are immobilized, amplified and sequenced. + An identifier of a lane within a flow cell of a sequencing machine, within which millions of sequences are immobilised, amplified and sequenced. 1.15 @@ -26649,17 +26649,17 @@ - Data model - A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) - - - - File format File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + + A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) + Data model + + + @@ -29498,7 +29498,7 @@ - + @@ -29510,7 +29510,7 @@ - + BioXSD XML format @@ -30003,13 +30003,13 @@ - + - + Format of a bibliographic reference. @@ -33078,8 +33078,8 @@ experiments employing a combination of technologies. SBOL 1.14 - SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. Synthetic Biology Open Language (SBOL) is an XML format for the specification and exchange of biological design information in synthetic biology. + SBOL introduces a standardised format for the electronic exchange of information on the structural and functional aspects of biological designs. @@ -33158,8 +33158,8 @@ experiments employing a combination of technologies. biom 1.15 + BIOM is a recognised standard for the Earth Microbiome Project, and is a project supported by Genomics Standards Consortium. Supported in QIIME, Mothur, MEGAN, etc. BIological Observation Matrix format - BIOM is a recognized standard for the Earth Microbiome Project, and is a project supported by Genomics Standards Consortium. Supported in QIIME, Mothur, MEGAN, etc. The BIological Observation Matrix (BIOM) is a format for representing biological sample by observation contingency tables in broad areas of comparative omics. The primary use of this format is to represent OTU tables and metagenome tables. @@ -33362,10 +33362,10 @@ experiments employing a combination of technologies. - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. - Function + Computational tool + Computational tool provides one or more operations. - + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. @@ -33374,10 +33374,10 @@ experiments employing a combination of technologies. - Computational tool - Computational tool provides one or more operations. + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + Function - + @@ -33568,14 +33568,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33619,14 +33619,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33693,14 +33693,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33954,14 +33954,14 @@ experiments employing a combination of technologies. - - + + - - + + Immunogenicity prediction @@ -34046,19 +34046,19 @@ experiments employing a combination of technologies. - + - - + + - - + + beta12orEarlier @@ -34349,14 +34349,14 @@ experiments employing a combination of technologies. - - + + - - + + Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. @@ -34609,32 +34609,32 @@ experiments employing a combination of technologies. - - + + - - + + - - + + - + - - + + beta12orEarlier @@ -34655,14 +34655,14 @@ experiments employing a combination of technologies. - - + + - - + + Identify and plot third base position variability in a nucleotide sequence. @@ -34694,14 +34694,14 @@ experiments employing a combination of technologies. - - + + - - + + Sequence distance matrix construction @@ -34842,12 +34842,6 @@ experiments employing a combination of technologies. - - - - - - @@ -34858,6 +34852,12 @@ experiments employing a combination of technologies. + + + + + + Sequence profile construction beta12orEarlier Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. @@ -34914,14 +34914,14 @@ experiments employing a combination of technologies. - - + + - - + + Sequence profile alignment @@ -34970,8 +34970,8 @@ experiments employing a combination of technologies. - - + + @@ -34982,8 +34982,8 @@ experiments employing a combination of technologies. - - + + beta12orEarlier @@ -35004,14 +35004,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35100,14 +35100,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35125,8 +35125,8 @@ experiments employing a combination of technologies. - - + + @@ -35137,8 +35137,8 @@ experiments employing a combination of technologies. - - + + Text data mining @@ -35176,8 +35176,8 @@ experiments employing a combination of technologies. - - + + @@ -35188,8 +35188,8 @@ experiments employing a combination of technologies. - - + + This includes predicting primers based on gene structure, promoters, exon-exon junctions, predicting primers that are conserved across multiple genomes or species, primers for for gene transcription profiling, for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs), for large scale sequencing, or for methylation PCRs. @@ -35224,19 +35224,19 @@ experiments employing a combination of technologies. - + - - + + - - + + Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. @@ -35279,25 +35279,13 @@ experiments employing a combination of technologies. Microarray data standardisation and normalisation - - - - - - - - - - - - - - + beta12orEarlier + true Standardize or normalize microarray data. - This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. - - + 1.16 + + @@ -35439,13 +35427,13 @@ experiments employing a combination of technologies. - + - + beta12orEarlier @@ -35464,14 +35452,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35490,14 +35478,14 @@ experiments employing a combination of technologies. - - + + - - + + WHATIF: UseResidueDB @@ -35540,14 +35528,14 @@ experiments employing a combination of technologies. - - + + - - + + Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. @@ -35602,13 +35590,13 @@ experiments employing a combination of technologies. - + - + @@ -35734,14 +35722,14 @@ experiments employing a combination of technologies. - - + + - - + + Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). @@ -35816,20 +35804,20 @@ experiments employing a combination of technologies. - + - - + + - - + + beta12orEarlier @@ -36210,13 +36198,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + @@ -36296,14 +36284,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -36320,7 +36308,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence mutation and randomisation beta12orEarlier - Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition. + Mutate a molecular sequence a specified amount or shuffle it to produce a randomised sequence with the same overall composition. @@ -36754,14 +36742,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Calculate the molecular weight of a protein sequence or fragments. @@ -36798,14 +36786,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Calculate pH-dependent properties from pKa calculations of a protein sequence. @@ -37065,14 +37053,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Sequence feature detection (nucleic acid) @@ -38162,14 +38150,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -38546,14 +38534,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + RNA secondary structure alignment generation @@ -39317,14 +39305,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Identify a plausible model of DNA substitution that explains a molecular (DNA or protein) sequence alignment. @@ -39371,14 +39359,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict families of genes and gene function based on their position in a phylogenetic tree. @@ -39552,14 +39540,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Visualise, format or render a molecular sequence or sequences such as a sequence alignment, possibly with sequence features or properties shown. @@ -39666,14 +39654,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -40896,14 +40884,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Structure analysis (protein) @@ -41057,14 +41045,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + This is a broad concept and is used a placeholder for other, more specific concepts. @@ -41084,14 +41072,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse known protein secondary structure data. @@ -41376,7 +41364,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Functional enrichment - @@ -41402,14 +41389,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict a network of gene regulation. @@ -41660,14 +41647,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Gene component prediction @@ -41804,14 +41791,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Identify or predict protein-protein interactions, interfaces, binding sites etc. @@ -41996,14 +41983,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + @@ -42095,14 +42082,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse nucleic acid tertiary structural data. @@ -42288,14 +42275,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict the interactions of proteins with other molecules. @@ -42787,14 +42774,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -43146,12 +43133,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - - - - - @@ -43162,6 +43143,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern + + + + + + Analyse a body of scientific text (typically a full text article from a scientific journal.) beta12orEarlier @@ -43192,14 +43179,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -43661,14 +43648,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + @@ -43706,7 +43693,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Localized reassembly + Localised reassembly Reconstruction of a sequence assembly in a localised area. 1.1 @@ -44735,13 +44722,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - + - + 1.4 @@ -44808,8 +44795,8 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs. - + @@ -44923,11 +44910,12 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Standardisation and normalisation - + + In the simplest normalisation means adjusting values measured on different scales to a common scale (often between 0.0 and 1.0), but can refer to more sophisticated adjustment whereby entire probability distributions of adjusted values are brought into alignment. Standardisation typically refers to an operation whereby a range of values are standardised to measure how many standard deviations a value is from its mean. Normalisation 1.6 + Standardize or normalize data by some statistical method. Standardisation - Standardize or normalize data. @@ -45436,7 +45424,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Chemical class enrichment - @@ -45663,20 +45650,20 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + - - + + 1.12 @@ -45793,14 +45780,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + 1.12 @@ -47670,7 +47657,7 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated Assembly The assembly of fragments of a DNA sequence to reconstruct the original sequence. beta12orEarlier - Assembly has two broad types, de-novo and re-sequencing. Re-sequencing is a specialized case of assembly, where an assembled (typically de-novo assembled) reference genome is available and is about 95% identical to the re-sequenced genome. All other cases of assembly are 'de-novo'. + Assembly has two broad types, de-novo and re-sequencing. Re-sequencing is a specialised case of assembly, where an assembled (typically de-novo assembled) reference genome is available and is about 95% identical to the re-sequenced genome. All other cases of assembly are 'de-novo'. @@ -49971,10 +49958,10 @@ positional features such as functional sites in nucleotide sequences.High-throughput sequencing Next-generation sequencing + Parallelised sequencing processes that are capable of sequencing many thousands of sequences simultaneously. beta13 true beta12orEarlier - Parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously. @@ -50942,8 +50929,8 @@ positional features such as functional sites in nucleotide sequences.Data security 1.3 + The protection of data, such as patient health data, from damage or unwanted access from unauthorised users. Data privacy - The protection of data, such as patient health data, from damage or unwanted access from unauthorized users. @@ -53365,7 +53352,7 @@ positional features such as functional sites in nucleotide sequences. - Personalized medicine + Personalised medicine 1.10 Health problems that are prevalent in tropical and subtropical regions.