diff --git a/releases/EDAM.owl b/releases/EDAM.owl index 324fe04..92f1e96 100644 --- a/releases/EDAM.owl +++ b/releases/EDAM.owl @@ -38,19 +38,19 @@ edam "EDAM" EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. operations "EDAM operations" + 01:07:2015 EDAM http://edamontology.org/ "EDAM relations and concept properties" application/rdf+xml EDAM_data http://edamontology.org/data_ "EDAM types of data" + 3581 concept_properties "EDAM concept properties" Jon Ison + 1.10 Matúš Kalaš Jon Ison, Matus Kalas, Herve Menager - 1.9 EDAM_format http://edamontology.org/format_ "EDAM data formats" - 3567 topics "EDAM topics" Hervé Ménager - 02:02:2015 EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. EDAM: An ontology of bioinformatics operations, types of data and identifiers, data formats, and topics @@ -362,16 +362,16 @@ - 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 + In very unusual cases. + true - + - 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 - + @@ -421,8 +421,8 @@ - In very unusual cases. true + In very unusual cases. @@ -449,17 +449,17 @@ - In very unusual cases. - true - - - - '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. OBO_REL:has_participant + + true + In very unusual cases. + + + @@ -491,8 +491,8 @@ - In very unusual cases. true + In very unusual cases. @@ -519,8 +519,8 @@ - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. OBO_REL:quality_of + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. @@ -548,23 +548,23 @@ - OBO_REL:function_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. + OBO_REL:function_of - In very unusual cases. - true - - - - 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 + + In very unusual cases. + true + + + @@ -609,16 +609,16 @@ - 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 inputs or input arguments. + 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 inputs or input arguments. + true + In very unusual cases. - + @@ -644,14 +644,14 @@ - true In very unusual cases. + true - 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. + OBO_REL:participates_in @@ -685,17 +685,17 @@ - OBO_REL:quality_of - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. - - - - true In very unusual cases. + + OBO_REL:quality_of + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. + + + @@ -710,25 +710,6 @@ - - - - Correlation - - - - - - - - Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data. - 1.7 - - - - - - @@ -768,6 +749,12 @@ + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Data set + + + + Data record EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). @@ -779,12 +766,6 @@ - - Data set - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - - - @@ -1438,7 +1419,7 @@ beta12orEarlier 1.8 true - Topic concerning secondary structure (predicted or real) of a protein. + Secondary structure (predicted or real) of a protein. @@ -1454,7 +1435,7 @@ Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. true beta12orEarlier - Topic concerning super-secondary structure of protein sequence(s). + Super-secondary structure of protein sequence(s). @@ -1784,9 +1765,9 @@ Protein structural motifs and surfaces - Topic concerning 3D structural motifs in a protein. true 1.8 + 3D structural motifs in a protein. beta12orEarlier Protein 3D motifs @@ -1815,8 +1796,8 @@ Protein features report (domains) true + structural domains or 3D folds in a protein or polypeptide chain. 1.8 - Topic concerning structural domains or 3D folds in a protein or polypeptide chain. beta12orEarlier @@ -2050,7 +2031,7 @@ DNA variation - Topic concerning stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. + stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. true 1.8 beta12orEarlier @@ -2102,7 +2083,7 @@ true 1.8 beta12orEarlier - Topic concerning PCR primers and hybridization oligos in a nucleic acid sequence. + PCR primers and hybridization oligos in a nucleic acid sequence. @@ -2116,8 +2097,8 @@ true beta12orEarlier + PCR experiments, e.g. quantitative real-time PCR. 1.8 - Topic concerning PCR experiments, e.g. quantitative real-time PCR. @@ -2211,8 +2192,8 @@ Microarray experiment report - Topic concerning microarray experiments including conditions, protocol, sample:data relationships etc. true + microarray experiments including conditions, protocol, sample:data relationships etc. 1.8 beta12orEarlier @@ -4511,13 +4492,13 @@ - + - + Unique name of a codon usage table. @@ -4547,7 +4528,7 @@ - Microarray experiment annotation ID + Experiment annotation ID @@ -6500,13 +6481,13 @@ - + - + A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information. @@ -7344,8 +7325,8 @@ true beta12orEarlier + regions of a nucleic acid sequence containing mobile genetic elements. 1.8 - Topic concerning regions of a nucleic acid sequence containing mobile genetic elements. @@ -7357,8 +7338,8 @@ Nucleic acid features report (PolyA signal or site) - Topic concerning regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. true + regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. 1.8 beta12orEarlier @@ -7388,8 +7369,8 @@ Nucleic acid features report (CpG island and isochore) 1.8 + CpG rich regions (isochores) in a nucleotide sequence. beta12orEarlier - Topic concerning CpG rich regions (isochores) in a nucleotide sequence. true @@ -7405,7 +7386,7 @@ beta12orEarlier true 1.8 - Topic concerning restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. + restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. @@ -7432,8 +7413,8 @@ Nucleic acid features report (splice sites) + splice sites in a nucleotide sequence or alternative RNA splicing events. beta12orEarlier - Topic concerning splice sites in a nucleotide sequence or alternative RNA splicing events. true 1.8 @@ -7448,9 +7429,9 @@ Nucleic acid features report (matrix/scaffold attachment sites) 1.8 + matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. true beta12orEarlier - Topic concerning matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. @@ -7493,8 +7474,8 @@ Gene features report (operon) true + operons (operators, promoters and genes) from a bacterial genome. 1.8 - Topic concerning operons (operators, promoters and genes) from a bacterial genome. beta12orEarlier @@ -7508,7 +7489,7 @@ Nucleic acid features report (promoters) 1.8 - Topic concerning whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. + whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. true beta12orEarlier @@ -7523,7 +7504,7 @@ Coding region beta12orEarlier - Topic concerning protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. + protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. 1.8 true @@ -7552,8 +7533,8 @@ Transcription factor binding sites + transcription factor binding sites (TFBS) in a DNA sequence. beta12orEarlier - Topic concerning transcription factor binding sites (TFBS) in a DNA sequence. true 1.8 @@ -7583,8 +7564,8 @@ Protein features report (signal peptides) - Topic concerning signal peptides or signal peptide cleavage sites in protein sequences. true + signal peptides or signal peptide cleavage sites in protein sequences. 1.8 beta12orEarlier @@ -7599,8 +7580,8 @@ Protein features report (cleavage sites) true - Topic concerning cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. 1.8 + cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. beta12orEarlier @@ -7615,7 +7596,7 @@ true beta12orEarlier - Topic concerning post-translation modifications in a protein sequence, typically describing the specific sites involved. + post-translation modifications in a protein sequence, typically describing the specific sites involved. 1.8 @@ -7628,10 +7609,10 @@ Protein features report (active sites) - Topic concerning catalytic residues (active site) of an enzyme. 1.8 true beta12orEarlier + catalytic residues (active site) of an enzyme. @@ -7643,8 +7624,8 @@ Protein features report (binding sites) - Topic concerning ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. beta12orEarlier + ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. true 1.8 @@ -7676,8 +7657,8 @@ true beta12orEarlier - Topic concerning RNA and DNA-binding proteins and binding sites in protein sequences. 1.8 + RNA and DNA-binding proteins and binding sites in protein sequences. @@ -9015,7 +8996,7 @@ true beta12orEarlier 1.8 - Topic concerning trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. + trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. @@ -10332,9 +10313,9 @@ Protein-protein interaction report + protein-protein interaction(s), including interactions between protein domains. beta12orEarlier true - Topic concerning protein-protein interaction(s), including interactions between protein domains. 1.8 @@ -10361,7 +10342,7 @@ Protein-nucleic acid interactions report true - Topic concerning protein-DNA/RNA interaction(s). + protein-DNA/RNA interaction(s). beta12orEarlier 1.8 @@ -10796,9 +10777,9 @@ Genetic information processing pathway report beta12orEarlier - Topic concerning genetic information processing pathways. 1.8 true + genetic information processing pathways. @@ -10810,8 +10791,8 @@ Environmental information processing pathway report - Topic concerning environmental information processing pathways. true + environmental information processing pathways. beta12orEarlier 1.8 @@ -10857,8 +10838,8 @@ true beta12orEarlier + disease pathways, typically of human disease. 1.8 - Topic concerning disease pathways, typically of human disease. @@ -10883,8 +10864,8 @@ Protein interaction networks - Topic concerning networks of protein interactions. 1.8 + networks of protein interactions. true beta12orEarlier @@ -13632,7 +13613,7 @@ Report - + You can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing. http://semanticscience.org/resource/SIO_000148 Document @@ -13889,8 +13870,8 @@ SNP + single nucleotide polymorphism (SNP) in a DNA sequence. true - Topic concerning single nucleotide polymorphism (SNP) in a DNA sequence. beta12orEarlier 1.8 @@ -14149,13 +14130,13 @@ - + - + Identifier of a codon usage table, for example a genetic code. @@ -14956,7 +14937,7 @@ 1.8 beta12orEarlier - Topic concerning chemical modification of a protein. + chemical modification of a protein. true @@ -16271,8 +16252,8 @@ 2D PAGE report - Topic concerning two-dimensional gel electrophoresis experiments, gels or spots in a gel. beta12orEarlier + two-dimensional gel electrophoresis experiments, gels or spots in a gel. 1.8 true @@ -16716,7 +16697,7 @@ Gene features report (exon) true - Topic concerning exons in a nucleotide sequences. + exons in a nucleotide sequences. 1.8 beta12orEarlier @@ -16749,8 +16730,8 @@ 1.8 beta12orEarlier + transcription of DNA into RNA including the regulation of transcription. true - Topic concerning transcription of DNA into RNA including the regulation of transcription. @@ -16968,7 +16949,7 @@ Nucleic acid features report (mutation) - Topic concerning DNA mutation. + DNA mutation. 1.8 true beta12orEarlier @@ -19233,7 +19214,7 @@ 1.8 true beta12orEarlier - Topic concerning disordered structure in a protein. + disordered structure in a protein. @@ -19686,7 +19667,7 @@ Gene features report (intron) - Topic concerning introns in a nucleotide sequences. + introns in a nucleotide sequences. true beta12orEarlier 1.8 @@ -20432,13 +20413,13 @@ - + - + Identifier of a lipid. @@ -20678,10 +20659,10 @@ Northern blot report - Topic concerning Northern Blot experiments. true beta12orEarlier 1.8 + Northern Blot experiments. @@ -20696,7 +20677,7 @@ 1.8 beta12orEarlier true - Topic concerning variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. + variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. @@ -20709,7 +20690,7 @@ Nucleic acid features report (microsatellite) true - Topic concerning microsatellite polymorphism in a DNA sequence. + microsatellite polymorphism in a DNA sequence. 1.8 beta12orEarlier @@ -20727,7 +20708,7 @@ beta12orEarlier true 1.8 - Topic concerning restriction fragment length polymorphisms (RFLP) in a DNA sequence. + restriction fragment length polymorphisms (RFLP) in a DNA sequence. @@ -20928,7 +20909,7 @@ Nucleic acid features report (polymorphism) true - Topic concerning DNA polymorphism. + DNA polymorphism. beta12orEarlier @@ -21930,8 +21911,8 @@ Protein features report (key folding sites) - Topic concerning key residues involved in protein folding. beta12orEarlier + key residues involved in protein folding. 1.8 true @@ -22479,7 +22460,7 @@ 1.8 beta13 - Topic concerning topological domains such as cytoplasmic regions in a protein. + topological domains such as cytoplasmic regions in a protein. true @@ -22524,7 +22505,7 @@ true beta13 - Topic concerning regions within a nucleic acid sequence containing a signal that alters a biological function. + regions within a nucleic acid sequence containing a signal that alters a biological function. 1.8 @@ -22537,8 +22518,8 @@ Nucleic acid features report (binding) + nucleic acids binding to some other molecule. 1.8 - Topic concerning nucleic acids binding to some other molecule. true beta13 This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). @@ -22554,9 +22535,9 @@ Nucleic acid repeats (report) true + repetitive elements within a nucleic acid sequence. 1.8 beta13 - Topic concerning repetitive elements within a nucleic acid sequence. @@ -22569,9 +22550,9 @@ Nucleic acid features report (replication and recombination) beta13 - Topic concerning DNA replication or recombination. true 1.8 + DNA replication or recombination. @@ -22602,8 +22583,8 @@ Protein features report (repeats) 1.8 + short repetitive subsequences (repeat sequences) in a protein sequence. beta13 - Topic concerning short repetitive subsequences (repeat sequences) in a protein sequence. true @@ -22700,8 +22681,8 @@ Nucleic acid features report (signal or transit peptide) true + coding sequences for a signal or transit peptide. 1.8 - Topic concerning coding sequences for a signal or transit peptide. beta13 @@ -22714,9 +22695,9 @@ Non-coding RNA - Topic concerning features of non-coding or functional RNA molecules, including tRNA and rRNA. beta13 true + features of non-coding or functional RNA molecules, including tRNA and rRNA. 1.8 @@ -22745,7 +22726,7 @@ Nucleic acid features report (STS) - Topic concerning sequence tagged sites (STS) in nucleic acid sequences. + sequence tagged sites (STS) in nucleic acid sequences. 1.8 true beta13 @@ -22866,8 +22847,8 @@ Mass spectrometry experiment 1.8 - Topic concerning mass spectrometry experiments. true + mass spectrometry experiments. beta13 @@ -22928,7 +22909,7 @@ 1.8 1.0 - Topic concerning sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. + sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. true @@ -23307,8 +23288,8 @@ RNAi report - Topic concerning RNAi experiments. 1.5 + RNAi experiments. true 1.8 @@ -23323,9 +23304,9 @@ Simulation experiment report 1.5 + biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. true 1.8 - Topic concerning biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. @@ -23606,6 +23587,34 @@ + + + + Reference sample report + + 1.10 + A report about a biosample. + Biosample report + + + + + + + + + + Gene Expression Atlas Experiment ID + + Accession number of an entry from the Gene Expression Atlas. + 1.10 + + + + + + + @@ -23973,7 +23982,7 @@ est2genome format - + beta12orEarlier Format of a report on exon-intron structure generated by EMBOSS est2genome. @@ -26237,16 +26246,16 @@ - File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. - File format + 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 - + - 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 denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + File format - + @@ -27704,6 +27713,7 @@ Format of a report on a particular locus, gene, gene system or groups of genes. beta12orEarlier + Gene features format @@ -27975,9 +27985,9 @@ Microarray experiment data format - + + Format for information about a microarray experimental per se (not the data generated from that experiment). beta12orEarlier - Format for microarray experimental data. @@ -28007,14 +28017,15 @@ Gene expression report format - + - + - Format for a report on gene expression. + Gene expression data format + Format of a file of gene expression data, e.g. a gene expression matrix or profile. beta12orEarlier @@ -28263,13 +28274,13 @@ - + - + Data format for the emission and transition counts of a hidden Markov model. @@ -28417,11 +28428,13 @@ Gene features (coding region) format - + beta12orEarlier Format used for report on coding regions in nucleotide sequences. - - + true + 1.10 + + @@ -29576,13 +29589,13 @@ - + - + Format of a bibliographic reference. @@ -30199,9 +30212,14 @@ MAGE-ML - + + + + + + 1.0 MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED). @@ -30216,9 +30234,14 @@ MAGE-TAB - + + + + + + MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED). 1.0 @@ -30981,17 +31004,13 @@ Gene expression data format - - - - - - - + + true + 1.10 1.7 Format of a file of gene expression data, e.g. a gene expression matrix or profile. - - + + @@ -31000,8 +31019,8 @@ Cytoscape input file format + - Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments. 1.7 @@ -31287,6 +31306,57 @@ + + + + IDAT + + + + + + + + + Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array. + 1.10 + + + + + + + + + + JPG + + + 1.10 + Joint Picture Group file format for lossy graphics file. + + Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type. + + + + + + + + + + + rcc + + + 1.10 + Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts. + + + + + + @@ -31329,10 +31399,10 @@ - Process - Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + Function - + Computational tool @@ -31341,10 +31411,10 @@ - Function - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + Process + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. - + @@ -31356,14 +31426,14 @@ - - + + - - + + beta12orEarlier @@ -31845,14 +31915,14 @@ - - + + - - + + WHATIF: SymShellTenXML @@ -31899,14 +31969,14 @@ - - + + - - + + Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. @@ -31927,14 +31997,14 @@ - - + + - - + + beta12orEarlier @@ -31954,14 +32024,14 @@ - - + + - - + + Sequence feature prediction @@ -32015,19 +32085,19 @@ - + - - + + - - + + beta12orEarlier @@ -32278,14 +32348,14 @@ - - + + - - + + Predict tertiary structure of a molecular (biopolymer) sequence. @@ -32448,14 +32518,14 @@ - - + + - - + + beta12orEarlier @@ -32595,32 +32665,32 @@ - - + + - + - - + + - + - - + + beta12orEarlier @@ -32680,14 +32750,14 @@ - - + + - - + + Sequence distance matrix construction @@ -32728,14 +32798,14 @@ - - + + - - + + The clusters may be output or used internally for some other purpose. @@ -32841,8 +32911,8 @@ - - + + @@ -32853,8 +32923,8 @@ - - + + Sequence profile construction @@ -32880,14 +32950,14 @@ - - + + - - + + Structural profile generation @@ -32907,12 +32977,6 @@ - - - - - - @@ -32923,6 +32987,12 @@ + + + + + + Sequence profile alignment beta12orEarlier See also 'Sequence alignment comparison'. @@ -32943,14 +33013,14 @@ - - + + - - + + beta12orEarlier @@ -32975,12 +33045,6 @@ - - - - - - @@ -32991,6 +33055,12 @@ + + + + + + Sequence-profile alignment construction Sequence-profile alignment generation beta12orEarlier @@ -33115,14 +33185,14 @@ - - + + - - + + beta12orEarlier @@ -33140,14 +33210,14 @@ - - + + - - + + @@ -33197,14 +33267,14 @@ - - + + - - + + PCR primer prediction @@ -33225,20 +33295,14 @@ - - - - - - - - + + @@ -33247,6 +33311,12 @@ + + + + + + Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. beta12orEarlier Microarray probe prediction @@ -33469,14 +33539,14 @@ - - + + - - + + beta12orEarlier @@ -33495,20 +33565,20 @@ - - + + - - + + - + Evaluate the quality or correctness a protein three-dimensional model. @@ -33616,13 +33686,13 @@ - + - + @@ -33751,14 +33821,14 @@ - - + + - - + + Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). @@ -33776,14 +33846,14 @@ - - + + - - + + beta12orEarlier @@ -33840,13 +33910,13 @@ - + - + @@ -34247,13 +34317,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + @@ -34829,14 +34899,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Calculate pH-dependent properties from pKa calculations of a protein sequence. @@ -35672,7 +35742,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment analysis (site correlation) - + Analyse correlations between sites in a molecular sequence alignment. This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. @@ -36135,14 +36205,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + @@ -36210,14 +36280,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -36238,14 +36308,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Nucleic acid folding family identification @@ -37705,13 +37775,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + @@ -37873,14 +37943,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Structure rendering @@ -38939,14 +39009,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -39285,14 +39355,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse known protein secondary structure data. @@ -39603,14 +39673,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict a network of gene regulation. @@ -39815,20 +39885,20 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - - + + Compare two or more molecular sequences. @@ -39876,14 +39946,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Gene and gene component prediction @@ -40015,14 +40085,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Identify or predict protein-protein interactions, interfaces, binding sites etc. @@ -40212,20 +40282,20 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - + Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. @@ -40501,14 +40571,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict the interactions of proteins with other molecules. @@ -40950,20 +41020,20 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - + beta12orEarlier @@ -41351,20 +41421,20 @@ 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.) @@ -41397,14 +41467,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -41751,14 +41821,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group. @@ -41849,20 +41919,20 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + - - + + 1.1 @@ -42636,14 +42706,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Infer a transcriptome sequence by analysis of short sequence reads. @@ -42692,13 +42762,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + @@ -42817,14 +42887,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Generate a checksum of a molecular sequence. @@ -42915,14 +42985,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Recognition of which format the given data is in. @@ -43375,7 +43445,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene expression correlation analysis - + 1.7 Gene co-expression network analysis @@ -43387,6 +43457,25 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern + + + + Correlation + + + + + + + + Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data. + 1.7 + + + + + + @@ -43788,6 +43877,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acids + The processing and analysis of nucleic acid sequence, structural and other data. Nucleic acid bioinformatics Nucleic acid analysis Nucleic acid informatics @@ -43796,7 +43886,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid physicochemistry http://purl.bioontology.org/ontology/MSH/D017422 beta12orEarlier - Topic concerning the processing and analysis of nucleic acid sequence, structural and other data. @@ -43808,12 +43897,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Proteins - Topic concerning archival, processing and analysis of protein data, typically molecular sequence and structural data. Protein bioinformatics Protein informatics Protein databases Protein analysis http://purl.bioontology.org/ontology/MSH/D020539 + Archival, processing and analysis of protein data, typically molecular sequence and structural data. beta12orEarlier @@ -43827,8 +43916,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Metabolites Metabolite structures - Topic concerning the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. This concept excludes macromolecules such as proteins and nucleic acids. + The structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. beta12orEarlier @@ -43845,8 +43934,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence databases Sequences http://purl.bioontology.org/ontology/MSH/D017421 - BioCatalogue:Sequence Analysis - Topic concerning the archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles. + The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles. @@ -43860,7 +43948,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure analysis Computational structural biology - Topic concerning the curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. + The curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. http://purl.bioontology.org/ontology/MSH/D015394 Structure analysis Structural bioinformatics @@ -43880,8 +43968,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure prediction - Topic concerning the prediction of molecular (secondary or tertiary) structure. beta12orEarlier + The prediction of molecular (secondary or tertiary) structure. @@ -43895,7 +43983,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier true - Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). + The alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). beta12orEarlier @@ -43912,15 +44000,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogeny reconstruction Phylogenetic stratigraphy beta12orEarlier - BioCatalogue:Tree Inference Phylogenetic dating Phylogenetic clocks - Topic concerning the study of evolutionary relationships amongst organisms. http://purl.bioontology.org/ontology/MSH/D010802 + The study of evolutionary relationships amongst organisms. Phylogenetic simulation - BioCatalogue:Phylogeny This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc. - BioCatalogue:Evolutionary Distance Measurements @@ -43935,8 +44020,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Topic concerning the study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. - BioCatalogue:Functional Genomics + The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. @@ -43948,15 +44032,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Ontology and terminology - - BioCatalogue:Ontology + Terminology beta12orEarlier http://purl.bioontology.org/ontology/MSH/D002965 Applied ontology Ontology - Topic concerning the conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource. - BioCatalogue:Ontology Lookup + The conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource. Ontologies @@ -43968,18 +44050,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Data search, query and retrieval + Information retrieval beta12orEarlier Data retrieval + The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information. This includes, for example, search, query and retrieval of molecular sequences and associated data. Data search - BioCatalogue:Identifier Retrieval - BioCatalogue:Data Retrieval - BioCatalogue:Sequence Retrieval - BioCatalogue:Image Retrieval - BioCatalogue:Structure Retrieval - Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information. + VT 1.3.3 Information retrieval Data query @@ -43991,11 +44069,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Bioinformatics - - + This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation. + VT 1.5.6 Bioinformatics + The archival, curation, processing and analysis of complex biological data. http://purl.bioontology.org/ontology/MSH/D016247 - Topic concerning the archival, curation, processing and analysis of complex biological data. beta12orEarlier @@ -44008,11 +44086,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data visualisation - + Data rendering - Topic for the rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data. - Data rendering and visualisation + Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data. + VT 1.2.5 Computer graphics beta12orEarlier + Computer graphics @@ -44024,8 +44103,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid thermodynamics - Topic concerning the study of the thermodynamic properties of a nucleic acid. true + The study of the thermodynamic properties of a nucleic acid. 1.3 @@ -44042,7 +44121,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern DNA melting Nucleic acid denaturation RNA alignment - Topic concerning the archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. + The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. RNA structure alignment beta12orEarlier Nucleic acid structure @@ -44060,7 +44139,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern RNA beta12orEarlier - Topic concerning RNA sequences and structures. + RNA sequences and structures. @@ -44087,13 +44166,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Mapping - Topic concerning the mapping of complete (typically nucleotide) sequences. Genetic linkage Linkage Linkage mapping Synteny DNA mapping beta12orEarlier + The mapping of complete (typically nucleotide) sequences. This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. @@ -44108,9 +44187,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier true - Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on. 1.3 Codon usage analysis + The study of codon usage in nucleotide sequence(s), genetic codes and so on. @@ -44123,7 +44202,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein expression Translation - Topic concerning the translation of mRNA into protein and subsequent protein processing in the cell. + The translation of mRNA into protein and subsequent protein processing in the cell. beta12orEarlier @@ -44137,14 +44216,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene finding - beta12orEarlier - Gene prediction - true 1.3 This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. - Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences. Gene discovery - BioCatalogue:Gene Prediction + Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences. + beta12orEarlier + Gene prediction + true @@ -44157,7 +44235,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Transcription 1.3 - Topic concerning the transcription of DNA into mRNA. + The transcription of DNA into mRNA. beta12orEarlier true @@ -44173,8 +44251,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern true beta12orEarlier - BioCatalogue:Promoter Prediction - Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). + Promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). beta13 @@ -44188,8 +44265,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid folding beta12orEarlier + The folding (in 3D space) of nucleic acid molecules. true - Topic concerning the folding (in 3D space) of nucleic acid molecules. beta12orEarlier @@ -44206,7 +44283,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern This includes the study of promoters, coding regions etc. beta12orEarlier Gene features - Topic concerning gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. + Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. @@ -44220,13 +44297,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Proteomics beta12orEarlier + Protein and peptide identification, especially in the study of whole proteomes of organisms. Protein and peptide identification Peptide identification Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues. http://purl.bioontology.org/ontology/MSH/D040901 - Topic concerning protein and peptide identification, especially in the study of whole proteomes of organisms. Protein expression - BioCatalogue:Proteomics @@ -44240,9 +44316,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structural genomics - BioCatalogue:Structural Genomics beta12orEarlier - Topic concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism. + The elucidation of the three dimensional structure for all (available) proteins in a given organism. @@ -44255,7 +44330,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein properties - Topic concerning the study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein. + The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein. Protein hydropathy Protein physicochemistry beta12orEarlier @@ -44271,6 +44346,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein interactions + Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. Protein-nucleic acid interactions Protein-RNA interaction This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. @@ -44278,9 +44354,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein-ligand interactions beta12orEarlier Protein-DNA interaction - BioCatalogue:Ligand Interaction - Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. - BioCatalogue:Protein Interaction @@ -44292,10 +44365,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein folding, stability and design - Topic concerning protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. Protein folding Protein stability beta12orEarlier + Protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. Protein residue interactions Protein design Rational protein design @@ -44310,7 +44383,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Two-dimensional gel electrophoresis - Topic concerning two-dimensional gel electrophoresis image and related data. + Two-dimensional gel electrophoresis image and related data. beta13 beta12orEarlier true @@ -44326,7 +44399,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Mass spectrometry beta12orEarlier - Topic concerning an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. + An analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. @@ -44339,7 +44412,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein microarrays - Topic concerning protein microarray data. + Protein microarray data. true beta12orEarlier beta13 @@ -44354,9 +44427,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydropathy - Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein. beta12orEarlier true + The study of the hydrophobic, hydrophilic and charge properties of a protein. 1.3 @@ -44371,7 +44444,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein targeting Protein sorting - Topic concerning the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. + The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. Protein localization beta12orEarlier @@ -44386,9 +44459,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein cleavage sites and proteolysis true - Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. beta12orEarlier 1.3 + Enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. @@ -44400,7 +44473,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein structure comparison - Topic concerning the comparison of two or more protein structures. + The comparison of two or more protein structures. beta12orEarlier true Use this concept for methods that are exclusively for protein structure. @@ -44435,9 +44508,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein interaction networks true + Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc. beta12orEarlier 1.3 - Topic concerning protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc. @@ -44450,9 +44523,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein-ligand interactions beta12orEarlier - Topic concerning protein-ligand (small molecule) interactions. true 1.3 + Protein-ligand (small molecule) interactions. @@ -44465,8 +44538,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein-nucleic acid interactions beta12orEarlier - Topic concerning protein-DNA/RNA interactions. 1.3 + Protein-DNA/RNA interactions. true @@ -44481,7 +44554,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.3 beta12orEarlier - Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. + The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. true @@ -44494,8 +44567,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern G protein-coupled receptors (GPCR) + G-protein coupled receptors (GPCRs). true - Topic concerning G-protein coupled receptors (GPCRs). beta12orEarlier beta12orEarlier @@ -44510,7 +44583,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Carbohydrates beta12orEarlier - Topic concerning carbohydrates, typically including structural information. + Carbohydrates, typically including structural information. @@ -44523,7 +44596,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Lipids beta12orEarlier - Topic concerning lipids and their structures. + Lipids and their structures. @@ -44535,8 +44608,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Small molecules + Small molecules of biological significance, typically archival, curation, processing and analysis of structural information. Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. - Topic concerning small molecules of biological significance, typically archival, curation, processing and analysis of structural information. CHEBI:23367 beta12orEarlier @@ -44566,14 +44639,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence composition, complexity and repeats + Sequence complexity Repeat sequences + The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences. beta12orEarlier - Sequence complexity - Low complexity sequences Sequence repeats - Topic concerning the archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences. + Low complexity sequences Sequence composition - BioCatalogue:Repeats @@ -44589,7 +44661,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Motifs true 1.3 - Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. + Conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. @@ -44601,11 +44673,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence comparison - BioCatalogue:Nucleotide Sequence Similarity The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. beta12orEarlier - BioCatalogue:Protein Sequence Similarity - Topic concerning the comparison of two or more molecular sequences, for example sequence alignment and clustering. + The comparison of two or more molecular sequences, for example sequence alignment and clustering. @@ -44618,10 +44688,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence sites, features and motifs Sequence features + The archival, detection, prediction and analysis of +positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. Functional sites Sequence motifs - Topic concerning the archival, detection, prediction and analysis of -positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. Sequence profiles Sequence sites HMMs @@ -44656,8 +44726,8 @@ positional features such as functional and other key sites, in molecular sequenc This includes systems that generate, process and analyse sequence clusters. beta12orEarlier true - Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities. 1.7 + The comparison and grouping together of molecular sequences on the basis of their similarities. Sequence clusters @@ -44675,9 +44745,9 @@ positional features such as functional and other key sites, in molecular sequenc Protein structural features Structural motifs Protein 3D motifs - Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. beta12orEarlier Protein structural motifs + Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. Protein surfaces @@ -44708,8 +44778,7 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier - Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. - BioCatalogue:Protein Structure Prediction + The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. @@ -44722,12 +44791,12 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid structure prediction + The folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. DNA structure prediction Nucleic acid design RNA structure prediction beta12orEarlier Nucleic acid folding - Topic concerning the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. @@ -44740,7 +44809,7 @@ positional features such as functional and other key sites, in molecular sequenc Ab initio structure prediction 1.7 - Topic concerning the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates. + The prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates. true beta12orEarlier @@ -44755,9 +44824,9 @@ positional features such as functional and other key sites, in molecular sequenc Homology modelling 1.4 + The modelling of the three-dimensional structure of a protein using known sequence and structural data. true beta12orEarlier - Topic concerning the modelling of the three-dimensional structure of a protein using known sequence and structural data. @@ -44772,9 +44841,9 @@ positional features such as functional and other key sites, in molecular sequenc This includes resources concerning flexibility and motion in protein and other molecular structures. Protein dynamics Molecular flexibility - Topic concerning the study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. Molecular motions beta12orEarlier + The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. @@ -44787,7 +44856,7 @@ positional features such as functional and other key sites, in molecular sequenc Molecular docking beta12orEarlier - Topic concerning the modelling the structure of proteins in complex with small molecules or other macromolecules. + The modelling the structure of proteins in complex with small molecules or other macromolecules. @@ -44799,9 +44868,9 @@ positional features such as functional and other key sites, in molecular sequenc Protein secondary structure prediction - Topic concerning the prediction of secondary or supersecondary structure of protein sequences. beta12orEarlier 1.3 + The prediction of secondary or supersecondary structure of protein sequences. true @@ -44817,8 +44886,8 @@ positional features such as functional and other key sites, in molecular sequenc 1.3 true + The prediction of tertiary structure of protein sequences. beta12orEarlier - Topic concerning the prediction of tertiary structure of protein sequences. @@ -44832,7 +44901,7 @@ positional features such as functional and other key sites, in molecular sequenc Protein fold recognition For example threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). - Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). + The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). beta12orEarlier @@ -44847,8 +44916,8 @@ positional features such as functional and other key sites, in molecular sequenc This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. beta12orEarlier - Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments). 1.7 + The alignment of molecular sequences or sequence profiles (representing sequence alignments). true @@ -44861,7 +44930,7 @@ positional features such as functional and other key sites, in molecular sequenc Structure alignment - Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). + The superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). This includes the generation, storage, analysis, rendering etc. of structure alignments. true 1.7 @@ -44879,8 +44948,8 @@ positional features such as functional and other key sites, in molecular sequenc Sequence-structure alignment 1.3 - Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). beta12orEarlier + The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). true @@ -44894,7 +44963,7 @@ positional features such as functional and other key sites, in molecular sequenc Sequence profiles and HMMs true - Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment. + Sequence profiles; typically a positional, numerical matrix representing a sequence alignment. beta12orEarlier 1.3 Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. @@ -44909,14 +44978,12 @@ positional features such as functional and other key sites, in molecular sequenc Phylogeny reconstruction - BioCatalogue:Evolutionary Distance Measurements - Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. + The reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. 1.3 true Currently too specific for the topic sub-ontology (but might be unobsoleted). beta12orEarlier - BioCatalogue:Tree Inference - + @@ -44929,7 +44996,7 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier - Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. + The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. @@ -44945,9 +45012,9 @@ positional features such as functional and other key sites, in molecular sequenc beta13 Polymerase chain reaction beta12orEarlier + Simulated polymerase chain reaction (PCR). PCR true - Topic concerning simulated polymerase chain reaction (PCR). @@ -44960,7 +45027,7 @@ positional features such as functional and other key sites, in molecular sequenc Sequence assembly Assembly - Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence. + The assembly of fragments of a DNA sequence to reconstruct the original sequence. beta12orEarlier This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. @@ -44976,11 +45043,11 @@ positional features such as functional and other key sites, in molecular sequenc http://purl.bioontology.org/ontology/MSH/D014644 + Stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. DNA variation Mutation Polymorphism beta12orEarlier - Topic concerning stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. @@ -44992,11 +45059,10 @@ positional features such as functional and other key sites, in molecular sequenc Microarrays - BioCatalogue:Microarrays true http://purl.bioontology.org/ontology/MSH/D046228 + Microarrays, for example, to process microarray data or design probes and experiments. 1.3 - Topic concerning microarrays, for example, to process microarray data or design probes and experiments. DNA microarrays beta12orEarlier @@ -45013,7 +45079,8 @@ positional features such as functional and other key sites, in molecular sequenc Computational pharmacology beta12orEarlier Pharmacoinformatics - Topic concerning the study of drugs and their effects or responses in living systems. + The study of drugs and their effects or responses in living systems. + VT 3.1.7 Pharmacology and pharmacy @@ -45027,16 +45094,15 @@ positional features such as functional and other key sites, in molecular sequenc Gene expression This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on. - BioCatalogue:Microarrays Gene expression profiling Expression profiling beta12orEarlier - Topic concerning the analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. http://edamontology.org/topic_0197 Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc. http://purl.bioontology.org/ontology/MSH/D015870 Gene expression analysis DNA microarrays + The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. Codon usage @@ -45050,8 +45116,8 @@ positional features such as functional and other key sites, in molecular sequenc Gene regulation - Topic concerning primarily the regulation of gene expression. beta12orEarlier + The regulation of gene expression. @@ -45065,7 +45131,7 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier - Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. + The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. @@ -45079,8 +45145,9 @@ positional features such as functional and other key sites, in molecular sequenc Medicinal chemistry + VT 3.1.4 Medicinal chemistry + The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes. This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. - Topic concerning the design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes. Drug design beta12orEarlier @@ -45096,9 +45163,9 @@ positional features such as functional and other key sites, in molecular sequenc Fish beta12orEarlier - Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation. true 1.3 + Information on a specific fish genome including molecular sequences, genes and annotation. @@ -45110,10 +45177,10 @@ positional features such as functional and other key sites, in molecular sequenc Flies - Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation. 1.3 true beta12orEarlier + Information on a specific fly genome including molecular sequences, genes and annotation. @@ -45125,9 +45192,9 @@ positional features such as functional and other key sites, in molecular sequenc Mice or rats + Information on a specific mouse or rat genome including molecular sequences, genes and annotation. The resource may be specific to a group of mice / rats or all mice / rats. beta12orEarlier - Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation. @@ -45139,10 +45206,10 @@ positional features such as functional and other key sites, in molecular sequenc Worms - Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation. true 1.3 beta12orEarlier + Information on a specific worm genome including molecular sequences, genes and annotation. @@ -45169,9 +45236,9 @@ positional features such as functional and other key sites, in molecular sequenc Data mining - Topic concerning the analysis of the biomedical and informatics literature. beta12orEarlier Text data mining + The analysis of the biomedical and informatics literature. Literature analysis Text mining Literature mining @@ -45187,7 +45254,7 @@ positional features such as functional and other key sites, in molecular sequenc Data deposition, annotation and curation - Topic concerning the organisation and maintenance of a collection of biological database entries (or other such entities) including the annotation of entries, typically with terms from a controlled vocabulary. + Deposition and curation of database accessions, including annotation, typically with terms from a controlled vocabulary. Database curation beta12orEarlier @@ -45200,13 +45267,16 @@ positional features such as functional and other key sites, in molecular sequenc - File management + Document, record and content management - Routine data management - Topic concerning basic manipulations of files or reports of generic biological data. - beta12orEarlier + Document management + File management This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. - Utility software + Content management + The management and manipulation of digital documents, including database records, files and reports. + VT 1.3.6 Multimedia, hypermedia + Record management + beta12orEarlier @@ -45221,7 +45291,7 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier beta12orEarlier true - Annotate a molecular sequence. + Annotation of a molecular sequence. @@ -45233,11 +45303,10 @@ positional features such as functional and other key sites, in molecular sequenc Genome annotation + Annotation of a genome. beta12orEarlier true beta12orEarlier - Annotate a genome. - BioCatalogue:Genome Annotation @@ -45254,13 +45323,13 @@ positional features such as functional and other key sites, in molecular sequenc ROESY NOESY Nuclear Overhauser Effect Spectroscopy + An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. HOESY beta12orEarlier Heteronuclear Overhauser Effect Spectroscopy Nuclear magnetic resonance spectroscopy Spectroscopy NMR spectroscopy - Topic concerning an analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. Rotational Frame Nuclear Overhauser Effect Spectroscopy @@ -45275,7 +45344,7 @@ positional features such as functional and other key sites, in molecular sequenc Sequence classification beta12orEarlier - Topic concerning the classification of molecular sequences based on some measure of their similarity. + The classification of molecular sequences based on some measure of their similarity. Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. @@ -45290,8 +45359,8 @@ positional features such as functional and other key sites, in molecular sequenc 1.3 true - Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc. beta12orEarlier + primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc. @@ -45305,9 +45374,9 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier true + Sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type. This includes comparison, discovery, recognition etc. of sequence motifs. beta12orEarlier - Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type. @@ -45321,7 +45390,7 @@ positional features such as functional and other key sites, in molecular sequenc Protein modifications GO:0006464 - Topic concerning protein chemical modifications, e.g. post-translational modifications. + Protein chemical modifications, e.g. post-translational modifications. Protein post-translational modification MOD:00000 EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) @@ -45337,16 +45406,14 @@ positional features such as functional and other key sites, in molecular sequenc Molecular interactions, pathways and networks - BioCatalogue:Pathway Retrieval Biological networks Network or pathway analysis beta13 Molecular interactions Biological models + Molecular interactions, biological pathways, networks and other models. Biological pathways - Topic concerning molecular interactions, biological pathways, networks and other models. http://edamontology.org/topic_3076 - BioCatalogue:Pathways @@ -45358,13 +45425,18 @@ positional features such as functional and other key sites, in molecular sequenc Informatics - - true - A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area. + + The study and practice of information processing and use of computer information systems. + VT 1.3.99 Other + Knowledge management + VT 1.3.4 Information management beta12orEarlier - beta12orEarlier - - + Information management + VT 1.3.5 Knowledge management + VT 1.3.3 Information retrieval + VT 1.3 Information sciences + Information science + @@ -45388,8 +45460,8 @@ positional features such as functional and other key sites, in molecular sequenc Laboratory information management - - Topic concerning laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. + + Laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. beta12orEarlier Laboratory resources @@ -45408,7 +45480,7 @@ positional features such as functional and other key sites, in molecular sequenc Tissue culture 1.3 true - Topic concerning general cell culture or data on a specific cell lines. + General cell culture or data on a specific cell lines. Cell culture beta12orEarlier @@ -45422,11 +45494,12 @@ positional features such as functional and other key sites, in molecular sequenc Ecology - Topic concerning the ecological and environmental sciences and especially the application of information technology (ecoinformatics). + The ecological and environmental sciences and especially the application of information technology (ecoinformatics). http://purl.bioontology.org/ontology/MSH/D004777 Ecological informatics - beta12orEarlier + VT 1.5.15 Ecology Computational ecology + beta12orEarlier Ecoinformatics Environmental science @@ -45445,7 +45518,7 @@ positional features such as functional and other key sites, in molecular sequenc SEM Scanning electron microscopy TEM - Topic concerning the study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light. + The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light. Transmission electron microscopy beta12orEarlier @@ -45465,9 +45538,9 @@ positional features such as functional and other key sites, in molecular sequenc Cell cycle beta13 - Topic concerning the cell cycle including key genes and proteins. beta12orEarlier true + The cell cycle including key genes and proteins. @@ -45480,7 +45553,7 @@ positional features such as functional and other key sites, in molecular sequenc Peptides and amino acids beta12orEarlier - Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides. + The physicochemical, biochemical or structural properties of amino acids or peptides. Amino acids Peptides @@ -45498,13 +45571,13 @@ positional features such as functional and other key sites, in molecular sequenc Cytoplasm Organelle genes and proteins Smooth endoplasmic reticulum - Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). beta12orEarlier Lysosome Centriole Ribosome Nucleus true + A specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). Mitochondria Golgi apparatus Rough endoplasmic reticulum @@ -45521,8 +45594,8 @@ positional features such as functional and other key sites, in molecular sequenc Ribosomes beta12orEarlier + Ribosomes, typically of ribosome-related genes and proteins. Ribosome genes and proteins - Topic concerning ribosomes, typically of ribosome-related genes and proteins. 1.3 true @@ -45553,8 +45626,8 @@ positional features such as functional and other key sites, in molecular sequenc Drug structures - Topic concerning the structures of drugs, drug target, their interactions and binding affinities. beta12orEarlier + The structures of drugs, drug target, their interactions and binding affinities. Target structures @@ -45570,7 +45643,7 @@ positional features such as functional and other key sites, in molecular sequenc This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism. beta12orEarlier - Topic concerning a specific organism, or group of organisms, used to study a particular aspect of biology. + A specific organism, or group of organisms, used to study a particular aspect of biology. Organisms @@ -45584,10 +45657,9 @@ positional features such as functional and other key sites, in molecular sequenc Genomics - BioCatalogue:Genomics http://purl.bioontology.org/ontology/MSH/D023281 - Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. beta12orEarlier + Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. @@ -45600,10 +45672,10 @@ positional features such as functional and other key sites, in molecular sequenc Gene families + Particular gene(s), gene family or other gene group or system and their encoded proteins. beta12orEarlier Gene family Gene system - Topic concerning particular gene(s), gene family or other gene group or system and their encoded proteins. Genes, gene family or system Gene and protein families @@ -45619,7 +45691,7 @@ positional features such as functional and other key sites, in molecular sequenc Chromosomes beta12orEarlier - Topic concerning chromosomes. + Study of chromosomes. @@ -45632,7 +45704,7 @@ positional features such as functional and other key sites, in molecular sequenc Genotype and phenotype Genotype and phenotype resources - Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. + The study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. Genotyping Phenotyping beta12orEarlier @@ -45648,10 +45720,10 @@ positional features such as functional and other key sites, in molecular sequenc Gene expression and microarray - Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc. true beta12orEarlier beta12orEarlier + Gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc. @@ -45668,8 +45740,8 @@ positional features such as functional and other key sites, in molecular sequenc This includes the design of primers for PCR and DNA amplification or the design of molecular probes. http://purl.bioontology.org/ontology/MSH/D015335 Gene design + Molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR). Probe design - Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR). in silico cloning Primer design Primers @@ -45685,9 +45757,10 @@ positional features such as functional and other key sites, in molecular sequenc Pathology - Topic concerning diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. + Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. beta12orEarlier Diseases + VT 3.1.6 Pathology @@ -45701,7 +45774,7 @@ positional features such as functional and other key sites, in molecular sequenc Specific protein resources 1.3 - Topic concerning a particular protein, protein family or other group of proteins. + A particular protein, protein family or other group of proteins. true Specific protein beta12orEarlier @@ -45717,7 +45790,8 @@ positional features such as functional and other key sites, in molecular sequenc Taxonomy beta12orEarlier - Topic concerning organism classification, identification and naming. + VT 1.5.25 Taxonomy + Organism classification, identification and naming. @@ -45730,8 +45804,8 @@ positional features such as functional and other key sites, in molecular sequenc Protein sequence analysis beta12orEarlier + Archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. 1.8 - Topic concerning archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. true @@ -45745,10 +45819,9 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid sequence analysis beta12orEarlier - BioCatalogue:Nucleotide Sequence Analysis 1.8 true - Topic concerning the archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. + The archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. @@ -45762,8 +45835,8 @@ positional features such as functional and other key sites, in molecular sequenc Repeat sequences true + The repetitive nature of molecular sequences. beta12orEarlier - Topic concerning the repetitive nature of molecular sequences. 1.3 @@ -45777,7 +45850,7 @@ positional features such as functional and other key sites, in molecular sequenc Low complexity sequences true - Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity. + The (character) complexity of molecular sequences, particularly regions of low complexity. 1.3 beta12orEarlier @@ -45791,7 +45864,7 @@ positional features such as functional and other key sites, in molecular sequenc Proteome - Topic concerning a specific proteome including protein sequences and annotation. + A specific proteome including protein sequences and annotation. beta12orEarlier beta13 true @@ -45808,7 +45881,7 @@ positional features such as functional and other key sites, in molecular sequenc DNA analysis beta12orEarlier - Topic concerning DNA sequences and structure, including processes such as methylation and replication. + DNA sequences and structure, including processes such as methylation and replication. The DNA sequences might be coding or non-coding sequences. @@ -45824,8 +45897,8 @@ positional features such as functional and other key sites, in molecular sequenc EST cDNA mRNA - Topic concerning protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames This includes expressed sequence tag (EST) or complementary DNA (cDNA) sequences. + Protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames beta12orEarlier @@ -45842,9 +45915,9 @@ positional features such as functional and other key sites, in molecular sequenc ncRNA Non-coding RNA Functional RNA + Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). Regulatory RNA Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA). - Topic concerning non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). beta12orEarlier @@ -45858,8 +45931,8 @@ positional features such as functional and other key sites, in molecular sequenc rRNA 1.3 + One or more ribosomal RNA (rRNA) sequences. true - Topic concerning one or more ribosomal RNA (rRNA) sequences. @@ -45873,7 +45946,7 @@ positional features such as functional and other key sites, in molecular sequenc 1.3 true - Topic concerning one or more transfer RNA (tRNA) sequences. + One or more transfer RNA (tRNA) sequences. @@ -45887,8 +45960,8 @@ positional features such as functional and other key sites, in molecular sequenc true beta12orEarlier - Topic concerning protein secondary structure or secondary structure alignments. 1.8 + Protein secondary structure or secondary structure alignments. This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. @@ -45902,7 +45975,7 @@ positional features such as functional and other key sites, in molecular sequenc RNA structure 1.3 - Topic concerning RNA secondary or tertiary structure and alignments. + RNA secondary or tertiary structure and alignments. beta12orEarlier true @@ -45917,8 +45990,8 @@ positional features such as functional and other key sites, in molecular sequenc Protein tertiary structure 1.8 - Topic concerning protein tertiary structures. true + Protein tertiary structures. beta12orEarlier @@ -45931,9 +46004,9 @@ positional features such as functional and other key sites, in molecular sequenc Nucleic acid classification + Classification of nucleic acid sequences and structures. 1.3 true - Topic concerning classification of nucleic acid sequences and structures. beta12orEarlier @@ -45946,11 +46019,11 @@ positional features such as functional and other key sites, in molecular sequenc Protein families - Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group. beta12orEarlier Protein sequence classification Protein secondary databases A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. + Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group. @@ -45963,10 +46036,9 @@ positional features such as functional and other key sites, in molecular sequenc Protein domains and folds - Topic concerning protein tertiary structural domains and folds. beta12orEarlier Protein folds - BioCatalogue:Domains + Protein tertiary structural domains and folds. Protein domains @@ -45981,8 +46053,8 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier true - Topic concerning nucleotide sequence alignments. 1.3 + Nucleotide sequence alignments. @@ -45995,10 +46067,10 @@ positional features such as functional and other key sites, in molecular sequenc Protein sequence alignment 1.3 + Protein sequence alignments. beta12orEarlier true A sequence profile typically represents a sequence alignment. - Topic concerning protein sequence alignments. @@ -46013,7 +46085,7 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier 1.3 true - Topic concerning the archival, detection, prediction and analysis of + The archival, detection, prediction and analysis of positional features such as functional sites in nucleotide sequences. @@ -46028,8 +46100,8 @@ positional features such as functional sites in nucleotide sequences.Protein sites and features beta12orEarlier + The detection, identification and analysis of positional features in proteins, such as functional sites. 1.3 - Topic concerning the detection, identification and analysis of positional features in proteins, such as functional sites. true @@ -46046,8 +46118,7 @@ positional features such as functional sites in nucleotide sequences. Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators. - BioCatalogue:Transcription Factors - Topic concerning proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. + Proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. Transcriptional regulatory sites TFBS Transcription factors @@ -46065,8 +46136,8 @@ positional features such as functional sites in nucleotide sequences.Phosphorylation sites 1.0 + Protein phosphorylation and phosphorylation sites in protein sequences. true - Topic concerning protein phosphorylation and phosphorylation sites in protein sequences. beta12orEarlier @@ -46081,7 +46152,7 @@ positional features such as functional sites in nucleotide sequences.Metabolic pathways beta12orEarlier - Topic concerning metabolic pathways. + Metabolic pathways. @@ -46093,7 +46164,7 @@ positional features such as functional sites in nucleotide sequences. Signaling pathways - Topic concerning signaling pathways. + Signaling pathways. Signal transduction pathways beta12orEarlier @@ -46121,7 +46192,7 @@ positional features such as functional sites in nucleotide sequences. Workflows - Topic concerning biological or biomedical analytical workflows or pipelines. + Biological or biomedical analytical workflows or pipelines. beta12orEarlier true 1.0 @@ -46135,7 +46206,7 @@ positional features such as functional sites in nucleotide sequences. Data types and objects - Topic concerning structuring data into basic types and (computational) objects. + Structuring data into basic types and (computational) objects. beta12orEarlier 1.0 true @@ -46165,7 +46236,7 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier true - Topic concerning mitochondria, typically of mitochondrial genes and proteins. + Mitochondria, typically of mitochondrial genes and proteins. 1.3 @@ -46178,11 +46249,14 @@ positional features such as functional sites in nucleotide sequences. Plants - Plant The resource may be specific to a plant, a group of plants or all plants. + Plant science + Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. Plant biology - Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. Botany + VT 1.5.22 Plant science + Plant + VT 1.5.10 Botany beta12orEarlier @@ -46196,8 +46270,9 @@ positional features such as functional sites in nucleotide sequences.Viruses Virology - Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. + VT 1.5.28 Virology beta12orEarlier + Viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. The resource may be specific to a virus, a group of viruses or all viruses. @@ -46212,9 +46287,10 @@ positional features such as functional sites in nucleotide sequences. Mycology beta12orEarlier - Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. The resource may be specific to a fungus, a group of fungi or all fungi. Yeast + VT 1.5.21 Mycology + Fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. @@ -46226,9 +46302,9 @@ positional features such as functional sites in nucleotide sequences. Pathogens + Pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. beta12orEarlier The resource may be specific to a pathogen, a group of pathogens or all pathogens. - Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. @@ -46240,8 +46316,8 @@ positional features such as functional sites in nucleotide sequences. Arabidopsis - Topic concerning Arabidopsis-specific data. beta12orEarlier + Arabidopsis-specific data. 1.3 true @@ -46255,9 +46331,9 @@ positional features such as functional sites in nucleotide sequences. Rice + Rice-specific data. true 1.3 - Topic concerning rice-specific data. beta12orEarlier @@ -46287,9 +46363,8 @@ positional features such as functional sites in nucleotide sequences. Comparative genomics - Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes. + The study (typically comparison) of the sequence, structure or function of multiple genomes. beta12orEarlier - BioCatalogue:Comparative Genomics @@ -46305,7 +46380,7 @@ positional features such as functional sites in nucleotide sequences. Transposons beta12orEarlier - Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. + Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. @@ -46317,10 +46392,10 @@ positional features such as functional sites in nucleotide sequences. Human disease + Human diseases, typically describing the genes, mutations and proteins implicated in disease. beta13 true beta12orEarlier - Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease. @@ -46332,12 +46407,13 @@ positional features such as functional sites in nucleotide sequences. Immunology - Topic concerning the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. + VT 3.1.3 Immunology Immunoinformatics - Computational immunology http://purl.bioontology.org/ontology/MSH/D007120 http://purl.bioontology.org/ontology/MSH/D007125 beta12orEarlier + Computational immunology + The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. @@ -46350,11 +46426,11 @@ positional features such as functional sites in nucleotide sequences. Membrane and lipoproteins + Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. beta12orEarlier Membrane proteins Lipoproteins Transmembrane proteins - Topic concerning lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. @@ -46366,8 +46442,8 @@ positional features such as functional sites in nucleotide sequences. Enzymes + Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. beta12orEarlier - Topic concerning proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. Enzymology @@ -46380,8 +46456,8 @@ positional features such as functional sites in nucleotide sequences. Primers + PCR primers and hybridization oligos in a nucleic acid sequence. Nucleic acid features (primers) - Topic concerning PCR primers and hybridization oligos in a nucleic acid sequence. beta12orEarlier Primer binding sites @@ -46401,7 +46477,7 @@ positional features such as functional sites in nucleotide sequences.PolyA signal A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. PolyA site - Topic concerning regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. + Regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. @@ -46416,7 +46492,7 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier Nucleic acid features (CpG island and isochore) - Topic concerning CpG rich regions (isochores) in a nucleotide sequence. + CpG rich regions (isochores) in a nucleotide sequence. @@ -46429,7 +46505,7 @@ positional features such as functional sites in nucleotide sequences. Restriction sites - Topic concerning restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. + Restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. Nucleic acid features (restriction sites) beta12orEarlier Nucleic acid restriction sites (report) @@ -46446,10 +46522,10 @@ positional features such as functional sites in nucleotide sequences.Splice sites - Topic concerning splice sites in a nucleotide sequence or alternative RNA splicing events. Nucleic acid features (splice sites) Nucleic acid report (RNA splicing) beta12orEarlier + Splice sites in a nucleotide sequence or alternative RNA splicing events. Nucleic acid report (RNA splice model) @@ -46465,7 +46541,7 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid features (matrix/scaffold attachment sites) beta12orEarlier - Topic concerning matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. + Matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. @@ -46479,10 +46555,10 @@ positional features such as functional sites in nucleotide sequences.Operon Gene features (operon) - Topic concerning operons (operators, promoters and genes) from a bacterial genome. beta12orEarlier Nucleic acid features (operon) The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. + Operons (operators, promoters and genes) from a bacterial genome. @@ -46495,9 +46571,9 @@ positional features such as functional sites in nucleotide sequences. Promoters + Whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. beta12orEarlier Nucleic acid features (promoters) - Topic concerning whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. @@ -46510,12 +46586,13 @@ positional features such as functional sites in nucleotide sequences. Structural biology - Topic concerning the molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. Structural assignment Structure determination This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. 1.3 This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy. Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen. + The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. + VT 1.5.24 Structural biology Structural determination @@ -46533,8 +46610,8 @@ positional features such as functional sites in nucleotide sequences.1.8 Protein features (membrane regions) This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. - Topic concerning trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. Intramembrane regions + Trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. Protein transmembrane regions Transmembrane regions @@ -46549,8 +46626,8 @@ positional features such as functional sites in nucleotide sequences. Structure comparison - Topic concerning the comparison of two or more molecular structures, for example structure alignment and clustering. This might involve comparison of secondary or tertiary (3D) structural information. + The comparison of two or more molecular structures, for example structure alignment and clustering. beta12orEarlier @@ -46565,8 +46642,7 @@ positional features such as functional sites in nucleotide sequences.Function analysis Protein function prediction - BioCatalogue:Function Prediction - Topic concerning the study of gene and protein function including the prediction of functional properties of a protein. + The study of gene and protein function including the prediction of functional properties of a protein. Protein function analysis beta12orEarlier @@ -46582,8 +46658,10 @@ positional features such as functional sites in nucleotide sequences.Prokaryotes and archae The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. + VT 1.5.2 Bacteriology + Bacteriology beta12orEarlier - Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation. + Specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation. @@ -46597,9 +46675,9 @@ positional features such as functional sites in nucleotide sequences. true 1.3 + Protein data resources. beta12orEarlier Protein data resources - Topic concerning protein data resources. @@ -46611,7 +46689,7 @@ positional features such as functional sites in nucleotide sequences. Structure determination - Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. + Experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. beta12orEarlier true 1.3 @@ -46627,7 +46705,8 @@ positional features such as functional sites in nucleotide sequences.Cell biology beta12orEarlier - Topic concerning cells, such as key genes and proteins involved in the cell cycle. + VT 1.5.11 Cell biology + Cells, such as key genes and proteins involved in the cell cycle. @@ -46656,8 +46735,8 @@ positional features such as functional sites in nucleotide sequences. true 1.3 - Topic concerning lipoproteins (protein-lipid assemblies). beta12orEarlier + Lipoproteins (protein-lipid assemblies). @@ -46671,7 +46750,6 @@ positional features such as functional sites in nucleotide sequences. true Visualise a phylogeny, for example, render a phylogenetic tree. - BioCatalogue:Tree Display beta12orEarlier beta12orEarlier @@ -46684,11 +46762,9 @@ positional features such as functional sites in nucleotide sequences. Cheminformatics - - + + The application of information technology to chemistry in biological research environment. Chemical informatics - BioCatalogue:Chemoinformatics - Topic concerning the application of information technology to chemistry in biological research environment. beta12orEarlier Chemoinformatics @@ -46704,17 +46780,13 @@ positional features such as functional sites in nucleotide sequences.Systems biology http://en.wikipedia.org/wiki/Systems_biology - BioCatalogue:Model Execution This includes databases of models and methods to construct or analyse a model. - BioCatalogue:Model Creation - Topic concerning the holistic modelling and analysis of complex biological systems and the interactions therein. Biological models http://purl.bioontology.org/ontology/MSH/D049490 - BioCatalogue:Model Analysis - BioCatalogue:Systems Biology beta12orEarlier - Biological system modelling Biological modelling + Biological system modelling + The holistic modelling and analysis of complex biological systems and the interactions therein. @@ -46725,12 +46797,11 @@ positional features such as functional sites in nucleotide sequences. - Statistics + Statistics and probability - Topic concerning the application of statistical methods to biological problems. Biostatistics + The application of statistical methods to biological problems. http://en.wikipedia.org/wiki/Biostatistics - BioCatalogue:Biostatistics beta12orEarlier http://purl.bioontology.org/ontology/MSH/D056808 @@ -46765,9 +46836,9 @@ positional features such as functional sites in nucleotide sequences.Comparative modeling Comparative modelling beta12orEarlier - Topic concerning the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. Homology modelling Molecular modeling + The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. @@ -46781,9 +46852,8 @@ positional features such as functional sites in nucleotide sequences. 1.2 beta12orEarlier - BioCatalogue:Function Prediction true - Topic concerning the prediction of functional properties of a protein. + The prediction of functional properties of a protein. @@ -46795,10 +46865,10 @@ positional features such as functional sites in nucleotide sequences. SNP + Single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. beta12orEarlier Single nucleotide polymorphism A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. - Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. @@ -46826,9 +46896,9 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid structure comparison + The comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. beta12orEarlier true - Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. beta12orEarlier Use this concept for methods that are exclusively for nucleic acid structures. @@ -46844,8 +46914,8 @@ positional features such as functional sites in nucleotide sequences.Exons Gene features (exon) - Topic concerning exons in a nucleotide sequences. beta12orEarlier + Exons in a nucleotide sequences. @@ -46865,9 +46935,9 @@ positional features such as functional sites in nucleotide sequences.This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. Enhancers (report) Terminators (report) + Transcription of DNA into RNA including the regulation of transcription. Ribosome binding sites (report) -10 signals (report) - Topic concerning transcription of DNA into RNA including the regulation of transcription. beta12orEarlier TATA signals (report) Attenuators (report) @@ -46886,8 +46956,8 @@ positional features such as functional sites in nucleotide sequences. Mutation annotation beta12orEarlier + DNA mutation. Nucleic acid features (mutation) - Topic concerning DNA mutation. @@ -46900,9 +46970,10 @@ positional features such as functional sites in nucleotide sequences. Oncology - Topic concerning the study of cancer, for example, genes and proteins implicated in cancer. beta12orEarlier + VT 3.2.16 Oncology Cancer + The study of cancer, for example, genes and proteins implicated in cancer. Cancer biology @@ -46918,9 +46989,9 @@ positional features such as functional sites in nucleotide sequences. Toxins - Topic concerning structural and associated data for toxic chemical substances. Targets beta12orEarlier + Structural and associated data for toxic chemical substances. @@ -46935,7 +47006,7 @@ positional features such as functional sites in nucleotide sequences. Gene features (intron) Nucleic acid features (intron) - Topic concerning introns in a nucleotide sequences. + Introns in a nucleotide sequences. beta12orEarlier @@ -46981,8 +47052,8 @@ positional features such as functional sites in nucleotide sequences. true 1.3 - Topic concerning biological nomenclature (naming), symbols and terminology. beta12orEarlier + Biological nomenclature (naming), symbols and terminology. @@ -46996,8 +47067,8 @@ positional features such as functional sites in nucleotide sequences. 1.3 true - Topic concerning the genes, gene variations and proteins involved in one or more specific diseases. beta12orEarlier + The genes, gene variations and proteins involved in one or more specific diseases. @@ -47010,9 +47081,9 @@ positional features such as functional sites in nucleotide sequences.Protein structure analysis Protein structure + Protein secondary or tertiary structural data and/or associated annotation. http://edamontology.org/topic_3040 beta12orEarlier - Topic concerning protein secondary or tertiary structural data and/or associated annotation. @@ -47027,7 +47098,7 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier true - Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general. + The human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general. @@ -47056,8 +47127,8 @@ positional features such as functional sites in nucleotide sequences. Yeast - Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation. beta12orEarlier + Yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation. true 1.3 @@ -47072,7 +47143,7 @@ positional features such as functional sites in nucleotide sequences.Eukaryotes Eukaryote - Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation. + Eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation. The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. beta12orEarlier @@ -47088,7 +47159,7 @@ positional features such as functional sites in nucleotide sequences. The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. beta12orEarlier - Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation. + Invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation. @@ -47101,7 +47172,7 @@ positional features such as functional sites in nucleotide sequences.Vertebrates The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. - Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. + Vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. beta12orEarlier @@ -47114,9 +47185,9 @@ positional features such as functional sites in nucleotide sequences. Unicellular eukaryotes + Unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation. beta12orEarlier The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. - Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation. @@ -47128,8 +47199,8 @@ positional features such as functional sites in nucleotide sequences. Protein structure alignment + Protein secondary or tertiary structure alignments. beta12orEarlier - Topic concerning protein secondary or tertiary structure alignments. true 1.3 @@ -47144,9 +47215,9 @@ positional features such as functional sites in nucleotide sequences.X-ray diffraction + The study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample. beta12orEarlier X-ray microscopy - Topic concerning the study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample. Crystallography X-ray crystallography @@ -47162,10 +47233,10 @@ positional features such as functional sites in nucleotide sequences.Ontologies, nomenclature and classification true + Conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics. 1.3 http://purl.bioontology.org/ontology/MSH/D002965 beta12orEarlier - Topic concerning conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics. @@ -47178,8 +47249,8 @@ positional features such as functional sites in nucleotide sequences.Immunoproteins, genes and antigens - Topic concerning immunity-related genes, proteins and their ligands. Immunopeptides + Immunity-related genes, proteins and their ligands. Antigens This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." beta12orEarlier @@ -47199,8 +47270,8 @@ positional features such as functional sites in nucleotide sequences. CHEBI:23367 beta12orEarlier - Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. beta12orEarlier + Specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. true @@ -47214,11 +47285,12 @@ positional features such as functional sites in nucleotide sequences.Toxicology - Topic concerning toxins and the adverse effects of these chemical substances on living organisms. - beta12orEarlier + Toxins and the adverse effects of these chemical substances on living organisms. + VT 3.1.9 Toxicology Toxicoinformatics - Computational toxicology Toxicology + beta12orEarlier + Computational toxicology @@ -47234,8 +47306,8 @@ positional features such as functional sites in nucleotide sequences.Next-generation sequencing beta13 true - Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously. beta12orEarlier + Parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously. @@ -47247,10 +47319,10 @@ positional features such as functional sites in nucleotide sequences. Structural clustering + The comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters. 1.7 Structure classification true - Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters. beta12orEarlier @@ -47264,7 +47336,7 @@ positional features such as functional sites in nucleotide sequences.Gene regulatory networks - Topic concerning gene regulatory networks. + Gene regulatory networks. beta12orEarlier @@ -47294,10 +47366,10 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid features (VNTR) Variable number of tandem repeat polymorphism + Variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. beta12orEarlier VNTR annotation VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. - Topic concerning variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. @@ -47312,9 +47384,9 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier Nucleic acid features (microsatellite) - Topic concerning microsatellite polymorphism in a DNA sequence. A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. Microsatellite annotation + Microsatellite polymorphism in a DNA sequence. @@ -47327,7 +47399,7 @@ positional features such as functional sites in nucleotide sequences. RFLP - Topic concerning restriction fragment length polymorphisms (RFLP) in a DNA sequence. + Restriction fragment length polymorphisms (RFLP) in a DNA sequence. An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. RFLP annotation beta12orEarlier @@ -47346,9 +47418,9 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid features (polymorphism) + DNA polymorphism. Polymorphism annotation beta12orEarlier - Topic concerning DNA polymorphism. @@ -47377,9 +47449,9 @@ positional features such as functional sites in nucleotide sequences.Primer or probe design 1.3 - Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes. true beta13 + The design of primers for PCR and DNA amplification or the design of molecular probes. @@ -47395,7 +47467,7 @@ positional features such as functional sites in nucleotide sequences.true 1.2 Structure data resources - Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. + Molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. @@ -47409,7 +47481,7 @@ positional features such as functional sites in nucleotide sequences. true beta13 - Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation. + Nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation. 1.2 @@ -47422,13 +47494,13 @@ positional features such as functional sites in nucleotide sequences. Sequence databases + Molecular sequence data resources, including sequence sites, alignments, motifs and profiles. true beta13 Sequence data resources Sequence data Sequence data resource 1.3 - Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles. @@ -47440,9 +47512,9 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid sequences + Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. beta13 1.3 - Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. true Nucleotide sequences @@ -47456,7 +47528,7 @@ positional features such as functional sites in nucleotide sequences. Protein sequences - Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles. + Protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles. beta13 1.3 true @@ -47484,8 +47556,9 @@ positional features such as functional sites in nucleotide sequences. Molecular biology + VT 1.5.4 Biochemistry and molecular biology beta13 - Topic concerning the molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. + The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. @@ -47499,9 +47572,9 @@ positional features such as functional sites in nucleotide sequences.Mammals true - Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. beta13 1.3 + Mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. @@ -47513,8 +47586,9 @@ positional features such as functional sites in nucleotide sequences. Biodiversity + The degree of variation of life forms within a given ecosystem, biome or an entire planet. beta13 - Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet. + VT 1.5.5 Biodiversity conservation http://purl.bioontology.org/ontology/MSH/D044822 @@ -47528,8 +47602,8 @@ positional features such as functional sites in nucleotide sequences. Sequence clusters and classification - Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity. This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. + The comparison, grouping together and classification of macromolecules on the basis of sequence similarity. Sequence families 1.3 true @@ -47546,12 +47620,10 @@ positional features such as functional sites in nucleotide sequences. Genetics - Topic concerning the study of genes, genetic variation and heredity in living organisms. - Gene database http://purl.bioontology.org/ontology/MSH/D005823 - Genetics data resources + The study of genes, genetic variation and heredity in living organisms. beta13 - Gene resource + Heredity @@ -47565,7 +47637,7 @@ positional features such as functional sites in nucleotide sequences.Quantitative genetics beta13 - Topic concerning the genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). + The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). @@ -47577,7 +47649,7 @@ positional features such as functional sites in nucleotide sequences. Population genetics - Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. + The distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. beta13 @@ -47591,8 +47663,8 @@ positional features such as functional sites in nucleotide sequences. Regulatory RNA - Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). 1.3 + Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). true beta13 @@ -47606,7 +47678,7 @@ positional features such as functional sites in nucleotide sequences. Documentation and help - Topic concerning the documentation of resources such as tools, services and databases and how to get help. + The documentation of resources such as tools, services and databases and how to get help. Help beta13 Documentation @@ -47622,9 +47694,9 @@ positional features such as functional sites in nucleotide sequences. Genetic organisation + The structural and functional organisation of genes and other genetic elements. 1.3 beta13 - Topic concerning the structural and functional organisation of genes and other genetic elements. true @@ -47636,13 +47708,12 @@ positional features such as functional sites in nucleotide sequences. Medical informatics - - - Topic concerning the application of information technology to health, disease and biomedicine. + Health informatics Clinical informatics Biomedical informatics Translational medicine + The application of information technology to health, disease and biomedicine. Healthcare informatics beta13 Health and disease @@ -47659,8 +47730,9 @@ positional features such as functional sites in nucleotide sequences. Developmental biology - Topic concerning how organisms grow and develop. + VT 1.5.14 Developmental biology beta13 + How organisms grow and develop. @@ -47674,7 +47746,7 @@ positional features such as functional sites in nucleotide sequences.Embryology beta13 - Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. + The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. @@ -47687,8 +47759,9 @@ positional features such as functional sites in nucleotide sequences. Anatomy + VT 3.1.1 Anatomy and morphology beta13 - Topic concerning the form and function of the structures of living organisms. + The form and function of the structures of living organisms. @@ -47703,8 +47776,8 @@ positional features such as functional sites in nucleotide sequences. Literature search beta13 + The scientific literature, reference information and documentation. Literature sources - Topic concerning the scientific literature, reference information and documentation. http://purl.bioontology.org/ontology/MSH/D011642 @@ -47718,9 +47791,24 @@ positional features such as functional sites in nucleotide sequences. Biology - Biological science + VT 1.5.8 Biology beta13 - Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on. + VT 1.5 Biological sciences + VT 1.5.23 Reproductive biology + Cryobiology + Biological rhythms + A particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on. + VT 1.5.7 Biological rhythm + Biological science + Aerobiology + VT 1.5.99 Other + Chronobiology + VT 1.5.13 Cryobiology + + VT 1.5.1 Aerobiology + VT 1.5.3 Behavioural biology + Reproductive biology + Behavioural biology @@ -47732,17 +47820,12 @@ positional features such as functional sites in nucleotide sequences. Data management - - Topic concerning the general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. - Databases - Data acquisition + + The development and use of architectures, policies, practices and procedures for management of data. beta13 + Data handling http://purl.bioontology.org/ontology/MSH/D030541 - Data handling - Information management - Databases - Knowledge management - Data processing + VT 1.3.1 Data management @@ -47756,9 +47839,9 @@ positional features such as functional sites in nucleotide sequences.Sequence feature detection 1.3 - Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences. true beta13 + The detection of the positional features, such as functional and other key sites, in molecular sequences. http://purl.bioontology.org/ontology/MSH/D058977 @@ -47771,8 +47854,8 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid feature detection + The detection of positional features such as functional sites in nucleotide sequences. true - Topic concerning the detection of positional features such as functional sites in nucleotide sequences. beta13 1.3 @@ -47786,8 +47869,8 @@ positional features such as functional sites in nucleotide sequences. Protein feature detection + The detection, identification and analysis of positional protein sequence features, such as functional sites. beta13 - Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites. 1.3 true @@ -47801,8 +47884,6 @@ positional features such as functional sites in nucleotide sequences. Biological system modelling - BioCatalogue:Model Analysis - BioCatalogue:Model Execution 1.2 true beta13 @@ -47818,7 +47899,7 @@ positional features such as functional sites in nucleotide sequences. Data acquisition - Topic concerning the acquisition of biological data. + The acquisition of data, typically measurements of physical systems using any type of sampling system, or by another other means. beta13 @@ -47832,10 +47913,10 @@ positional features such as functional sites in nucleotide sequences.Genes and proteins resources 1.3 - Topic concerning specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. Gene family beta13 Gene and protein families + Specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. true @@ -47849,8 +47930,8 @@ positional features such as functional sites in nucleotide sequences.Protein topological domains + Topological domains such as cytoplasmic regions in a protein. Protein features (topological domains) - Topic concerning topological domains such as cytoplasmic regions in a protein. 1.8 @@ -47864,8 +47945,8 @@ positional features such as functional sites in nucleotide sequences. Protein variants + protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. beta13 - Topic concerning protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. @@ -47880,8 +47961,8 @@ positional features such as functional sites in nucleotide sequences. beta13 - Topic concerning regions within a nucleic acid sequence containing a signal that alters a biological function. Nucleic acid features (expression signal) + Regions within a nucleic acid sequence containing a signal that alters a biological function. @@ -47897,8 +47978,8 @@ positional features such as functional sites in nucleotide sequences. This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). beta13 - Topic concerning nucleic acids binding to some other molecule. Nucleic acid features (binding) + Nucleic acids binding to some other molecule. @@ -47913,7 +47994,7 @@ positional features such as functional sites in nucleotide sequences. beta13 This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. - Topic concerning repetitive elements within a nucleic acid sequence. + Repetitive elements within a nucleic acid sequence. @@ -47926,11 +48007,11 @@ positional features such as functional sites in nucleotide sequences. DNA replication and recombination + DNA replication or recombination. This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. Nucleosome exclusion sequences Nucleic acid features (replication and recombination) beta13 - Topic concerning DNA replication or recombination. @@ -47943,10 +48024,10 @@ positional features such as functional sites in nucleotide sequences. Signal or transit peptide - Topic concerning coding sequences for a signal or transit peptide. beta13 Nucleic acid features (signal or transit peptide) A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. + Coding sequences for a signal or transit peptide. @@ -47960,9 +48041,9 @@ positional features such as functional sites in nucleotide sequences.Sequence tagged sites Nucleic acid features (STS) - Topic concerning sequence tagged sites (STS) in nucleic acid sequences. beta13 Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. + Sequence tagged sites (STS) in nucleic acid sequences. @@ -47975,11 +48056,11 @@ positional features such as functional sites in nucleotide sequences. Sequencing - Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. http://purl.bioontology.org/ontology/MSH/D059014 1.1 NGS Next generation sequencing + The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. Next gen sequencing @@ -47998,8 +48079,8 @@ positional features such as functional sites in nucleotide sequences.Chip sequencing Chip seq 1.1 + The analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. Chip-sequencing - Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. @@ -48032,8 +48113,8 @@ positional features such as functional sites in nucleotide sequences. DNA methylation - Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. true + DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. 1.3 http://purl.bioontology.org/ontology/MSH/D019175 1.1 @@ -48048,7 +48129,7 @@ positional features such as functional sites in nucleotide sequences. Metabolomics - Topic concerning the systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism. + The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism. http://purl.bioontology.org/ontology/MSH/D055432 1.1 @@ -48067,7 +48148,7 @@ positional features such as functional sites in nucleotide sequences.Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. 1.1 http://purl.bioontology.org/ontology/MSH/D057890 - Topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc. + The study of the epigenetic modifications of a whole cell, tissue, organism etc. @@ -48085,8 +48166,8 @@ positional features such as functional sites in nucleotide sequences.Ecogenomics Community genomics Environmental genomics - Topic concerning the study of genetic material recovered from environmental samples, and associated environmental data. 1.1 + The study of genetic material recovered from environmental samples, and associated environmental data. @@ -48101,7 +48182,7 @@ positional features such as functional sites in nucleotide sequences. 1.1 - Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. + Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. Genomic structural variation @@ -48115,7 +48196,7 @@ positional features such as functional sites in nucleotide sequences.DNA packaging beta12orEarlier - Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. + DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. http://purl.bioontology.org/ontology/MSH/D042003 @@ -48145,9 +48226,9 @@ positional features such as functional sites in nucleotide sequences.RNA-Seq alignment true - Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. 1.3 RNA-seq alignment + The alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. beta12orEarlier @@ -48162,8 +48243,8 @@ positional features such as functional sites in nucleotide sequences. true 1.3 - Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. 1.1 + Experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. ChIP-chip @@ -48176,11 +48257,9 @@ positional features such as functional sites in nucleotide sequences. Data security - Topic concerning the protection of data, for example, patient health data. - Privacy 1.3 - Security - Security + Data privacy + The protection of data, such as patient health data, from damage or unwanted access from unauthorized users. @@ -48194,9 +48273,9 @@ positional features such as functional sites in nucleotide sequences. samples biobanking - Topic concerning biological samples and specimens. 1.3 biosamples + Biological samples and specimens. Specimen collections @@ -48211,10 +48290,11 @@ positional features such as functional sites in nucleotide sequences.Biochemistry + VT 1.5.4 Biochemistry and molecular biology Chemical biology 1.3 - Topic concerning chemical substances and physico-chemical processes and that occur within living organisms. Biological chemistry + Chemical substances and physico-chemical processes and that occur within living organisms. @@ -48228,7 +48308,7 @@ positional features such as functional sites in nucleotide sequences.Phylogenetics - Topic concerning the study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). + The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). 1.3 http://purl.bioontology.org/ontology/MSH/D010802 @@ -48260,8 +48340,8 @@ positional features such as functional sites in nucleotide sequences. Biotechnology - Topic concerning the exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. 1.3 + The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. @@ -48275,7 +48355,7 @@ positional features such as functional sites in nucleotide sequences.Phenomics - Topic concerning phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. + Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. 1.3 @@ -48289,8 +48369,9 @@ positional features such as functional sites in nucleotide sequences. Evolutionary biology - Topic concerning the evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. + VT 1.5.16 Evolutionary biology 1.3 + The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. @@ -48303,8 +48384,9 @@ positional features such as functional sites in nucleotide sequences. Physiology + The functions of living organisms and their constituent parts. 1.3 - Topic concerning the functions of living organisms and their constituent parts. + VT 3.1.8 Physiology @@ -48317,8 +48399,9 @@ positional features such as functional sites in nucleotide sequences. Microbiology - Topic concerning the biology of microorganisms. + The biology of microorganisms. 1.3 + VT 1.5.20 Microbiology @@ -48331,9 +48414,8 @@ positional features such as functional sites in nucleotide sequences. Parasitology - Topic concerning the biology of parasites. - Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. 1.3 + The biology of parasites. @@ -48346,10 +48428,16 @@ positional features such as functional sites in nucleotide sequences. Medicine - Experimental medicine - Topic concerning research in support of healing by diagnosis, treatment, and prevention of disease. + General medicine + Research in support of healing by diagnosis, treatment, and prevention of disease. 1.3 + VT 3.1 Basic medicine + VT 3.2.9 General and internal medicine + Experimental medicine Biomedical research + Clinical medicine + VT 3.2 Clinical medicine + Internal medicine @@ -48364,7 +48452,8 @@ positional features such as functional sites in nucleotide sequences. Neuroscience 1.3 - Topic concerning the study of the nervous system and brain; its anatomy, physiology and function. + The study of the nervous system and brain; its anatomy, physiology and function. + VT 3.1.5 Neuroscience @@ -48377,6 +48466,7 @@ positional features such as functional sites in nucleotide sequences. Public health and epidemiology + VT 3.3.1 Epidemiology Topic concerning the the patterns, cause, and effect of disease within populations. 1.3 Public health @@ -48395,7 +48485,8 @@ positional features such as functional sites in nucleotide sequences. 1.3 - Topic concerning the use of physics to study biological system. + VT 1.5.9 Biophysics + The use of physics to study biological system. @@ -48409,12 +48500,14 @@ positional features such as functional sites in nucleotide sequences.Computational biology - BioCatalogue:Model Execution + VT 1.5.19 Mathematical biology + VT 1.5.12 Computational biology This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology). Mathematical biology - Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. + VT 1.5.26 Theoretical biology Theoretical biology 1.3 + The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. Biomathematics @@ -48429,9 +48522,9 @@ positional features such as functional sites in nucleotide sequences.Transcriptomics + The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. Transcriptome 1.3 - Topic concerning the analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. @@ -48444,8 +48537,24 @@ positional features such as functional sites in nucleotide sequences. Chemistry + VT 1.7.10 Polymer science + VT 1.7.7 Mathematical chemistry + VT 1.7.3 Colloid chemistry 1.3 - Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances. + Mathematical chemistry + Physical chemistry + VT 1.7.9 Physical chemistry + Polymer science + Chemical science + Organic chemistry + VT 1.7.6 Inorganic and nuclear chemistry + VT 1.7 Chemical sciences + VT 1.7.5 Electrochemistry + Inorganic chemistry + VT 1.7.2 Chemistry + Nuclear chemistry + VT 1.7.8 Organic chemistry + The composition and properties of matter, reactions, and the use of reactions to create new substances. @@ -48458,8 +48567,10 @@ positional features such as functional sites in nucleotide sequences. Mathematics - Topic concerning the is the study of numbers (quantity) and other topics including structure, space, and change. + The study of numbers (quantity) and other topics including structure, space, and change. + VT:1.1 Mathematics Maths + VT 1.1.99 Other 1.3 @@ -48474,7 +48585,9 @@ positional features such as functional sites in nucleotide sequences.Computer science 1.3 - Topic concerning the theory and practical use of computer systems. + VT 1.2 Computer sciences + VT 1.2.99 Other + The theory and practical use of computer systems. @@ -48487,7 +48600,7 @@ positional features such as functional sites in nucleotide sequences. Physics - Topic concerning the study of matter, space and time, and related concepts such as energy and force. + The study of matter, space and time, and related concepts such as energy and force. 1.3 @@ -48502,7 +48615,7 @@ positional features such as functional sites in nucleotide sequences.RNA splicing - Topic concerning RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons. + RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons. This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. 1.3 @@ -48516,8 +48629,8 @@ positional features such as functional sites in nucleotide sequences. Molecular genetics - Topic concerning the structure and function of genes at a molecular level. 1.3 + The structure and function of genes at a molecular level. @@ -48530,12 +48643,13 @@ positional features such as functional sites in nucleotide sequences. Respiratory medicine - Respiratory disease + VT 3.2.25 Respiratory systems + Pulmonology + The study of respiratory system. Pulmonary medicine + Respiratory disease 1.3 Pulmonary disorders - Pulmonology - Topic concerning the study of respiratory system. @@ -48548,10 +48662,10 @@ positional features such as functional sites in nucleotide sequences. Metabolic disease + The study of metabolic diseases. 1.4 1.3 true - Topic concerning the study of metabolic diseases. @@ -48564,8 +48678,9 @@ positional features such as functional sites in nucleotide sequences.Infectious disease Transmissable disease + VT 3.3.4 Infectious diseases Communicable disease - Topic concerning the branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions). + The branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions). 1.3 @@ -48580,7 +48695,7 @@ positional features such as functional sites in nucleotide sequences.Rare diseases 1.3 - Topic concerning the study of rare diseases. + The study of rare diseases. @@ -48595,6 +48710,7 @@ positional features such as functional sites in nucleotide sequences. 1.3 + VT 1.7.4 Computational chemistry Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. @@ -48608,9 +48724,9 @@ positional features such as functional sites in nucleotide sequences. Neurology - Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. Neurological disorders 1.3 + The branch of medicine that deals with the anatomy, functions and disorders of the nervous system. @@ -48623,11 +48739,13 @@ positional features such as functional sites in nucleotide sequences. Cardiology - Cardiovascular medicine + Cardiovascular disease + VT 3.2.4 Cardiac and Cardiovascular systems 1.3 - Topic concerning the diseases and abnormalities of the heart and circulatory system. + Cardiovascular medicine Heart disease - Cardiovascular disease + VT 3.2.22 Peripheral vascular disease + The diseases and abnormalities of the heart and circulatory system. @@ -48641,8 +48759,8 @@ positional features such as functional sites in nucleotide sequences.Drug discovery + The discovery and design of drugs or potential drug compounds. This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. - Topic concerning the discovery and design of drugs or potential drug compounds. 1.3 @@ -48658,7 +48776,7 @@ positional features such as functional sites in nucleotide sequences. biobanking 1.3 - Topic concerning repositories of biological samples, typically human, for basic biological and clinical research. + Repositories of biological samples, typically human, for basic biological and clinical research. Tissue collection @@ -48673,7 +48791,7 @@ positional features such as functional sites in nucleotide sequences.Mouse clinic 1.3 - Topic concerning laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. + Laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. @@ -48686,8 +48804,8 @@ positional features such as functional sites in nucleotide sequences. Microbial collection + Collections of microbial cells including bacteria, yeasts and moulds. 1.3 - Topic concerning collections of microbial cells including bacteria, yeasts and moulds. @@ -48700,8 +48818,8 @@ positional features such as functional sites in nucleotide sequences. Cell culture collection - Topic concerning collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells. 1.3 + Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells. @@ -48715,7 +48833,7 @@ positional features such as functional sites in nucleotide sequences.Clone library 1.3 - Topic concerning collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. + Collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. @@ -48728,7 +48846,7 @@ positional features such as functional sites in nucleotide sequences. Translational medicine - Topic concerning 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. + 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. 1.3 @@ -48744,7 +48862,7 @@ positional features such as functional sites in nucleotide sequences. Translational medicine Chemical library - Topic concerning collections of chemicals, typically for use in high-throughput screening experiments. + Collections of chemicals, typically for use in high-throughput screening experiments. Compound library Chemical screening 1.3 @@ -48762,6 +48880,8 @@ positional features such as functional sites in nucleotide sequences. Topic concerning biological science that is (typically) performed in the context of medicine. + VT 3.3 Health sciences + Health science 1.3 @@ -48775,8 +48895,8 @@ positional features such as functional sites in nucleotide sequences. Data identity and mapping + Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases. 1.3 - Topic concerning the identity of biological data and the mapping of entities in different databases. @@ -48791,7 +48911,7 @@ positional features such as functional sites in nucleotide sequences. 1.3 Sequence database search - Topic concerning the search and retrieval from a database on the basis of molecular sequence similarity. + The search and retrieval from a database on the basis of molecular sequence similarity. @@ -48805,7 +48925,7 @@ positional features such as functional sites in nucleotide sequences. Diagnostic markers 1.4 - Topic concerning objective indicators of biological state often used to assess health, and determinate treatment. + Objective indicators of biological state often used to assess health, and determinate treatment. @@ -48817,7 +48937,7 @@ positional features such as functional sites in nucleotide sequences. Laboratory techniques - Topic concerning the procedures used to conduct an experiment. + The procedures used to conduct an experiment. Lab techniques 1.4 @@ -48830,10 +48950,13 @@ positional features such as functional sites in nucleotide sequences. - Data analysis + Data architecture, analysis and design - Topic concerning the process of systematically applying statistical and / or logical techniques to describe and illustrate, condense and recap, and evaluate data. + The development of policies, models and standards that cover data acquisitioin, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data. + Data analysis + Data design 1.4 + Data architecture @@ -48844,10 +48967,14 @@ positional features such as functional sites in nucleotide sequences. - Data integration + Data integration and warehousing - Topic concerning the combination of data from different sources to provide users with a unified view of these data. + The combination and integration of data from different sources, for example into a central repository or warehouse, to provide users with a unified view of these data. + + + Data integration 1.4 + Data warehousing @@ -48860,9 +48987,9 @@ positional features such as functional sites in nucleotide sequences. Biomaterials + Any matter, surface or construct that interacts with a biological system. Diagnostic markers 1.4 - Topic concerning any matter, surface or construct that interacts with a biological system. @@ -48877,7 +49004,7 @@ positional features such as functional sites in nucleotide sequences. 1.4 - Topic concerning the use of synthetic chemistry to study and manipulate biological systems. + The use of synthetic chemistry to study and manipulate biological systems. @@ -48891,7 +49018,8 @@ positional features such as functional sites in nucleotide sequences.Analytical chemistry 1.4 - Topic concerning the study of the separation, identification, and quantification of the chemical components of natural and artificial materials. + The study of the separation, identification, and quantification of the chemical components of natural and artificial materials. + VT 1.7.1 Analytical chemistry @@ -48905,8 +49033,8 @@ positional features such as functional sites in nucleotide sequences.Synthetic chemistry Synthetic organic chemistry + The use of chemistry to create new compounds. 1.4 - Topic concerning the use of chemistry to create new compounds. @@ -48917,11 +49045,20 @@ positional features such as functional sites in nucleotide sequences. - Computer programming + Software engineering - Topic concerning the process that leads from an original formulation of a computing problem to executable programs. - 1.4 + VT 1.2.1 Algorithms + Programming languages + VT 1.2.7 Data structures Software development + Software engineering + Computer programming + 1.4 + 1.2.12 Programming languages + The process that leads from an original formulation of a computing problem to executable programs. + Data structures + Algorithms + VT 1.2.14 Software engineering @@ -48935,8 +49072,8 @@ positional features such as functional sites in nucleotide sequences.Drug development 1.4 - Topic concerning the process of bringing a new drug to market once a lead compounds has been identified through drug discovery. Medicine development + The process of bringing a new drug to market once a lead compounds has been identified through drug discovery. Drug development science Medicines development @@ -48951,9 +49088,9 @@ positional features such as functional sites in nucleotide sequences. Drug formulation and delivery + The process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. Drug delivery Drug formulation - Topic concerning the process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. 1.4 @@ -48969,10 +49106,10 @@ positional features such as functional sites in nucleotide sequences. Pharmacodynamics Pharmacokinetics - Topic concerning the study of how a drug interacts with the body. Drug distribution 1.4 Drug excretion + The study of how a drug interacts with the body. Drug absorption ADME Drug metabolism @@ -48990,10 +49127,11 @@ positional features such as functional sites in nucleotide sequences.Medicines research and development Medicine research and development + The discovery, development and approval of medicines. Health care research Drug discovery and development 1.4 - Topic concerning the discovery, development and approval of medicines. + Health care science @@ -49008,7 +49146,7 @@ positional features such as functional sites in nucleotide sequences. 1.4 Drug safety - Topic concerning the safety (or lack) of drugs and other medical interventions. + The safety (or lack) of drugs and other medical interventions. @@ -49023,7 +49161,7 @@ positional features such as functional sites in nucleotide sequences. 1.4 Pharmacovigilence concerns safety once a drug has gone to market. - Topic concerning the detection, assesment, understanding and prevention of adverse effects of medicines. + The detection, assesment, understanding and prevention of adverse effects of medicines. @@ -49036,7 +49174,7 @@ positional features such as functional sites in nucleotide sequences. Preclinical and clinical studies - Topic concerning the testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities. + The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities. Preclinical studies 1.4 Clinical studies @@ -49057,7 +49195,7 @@ positional features such as functional sites in nucleotide sequences.1.4 Microscopy Diffraction experiment - Topic concerning the visual representation of an object. + The visual representation of an object. @@ -49070,8 +49208,8 @@ positional features such as functional sites in nucleotide sequences. Biological imaging + The use of imaging techniques to understand biology. 1.4 - Topic concerning the use of imaging techniques to understand biology. @@ -49084,8 +49222,13 @@ positional features such as functional sites in nucleotide sequences. Medical imaging - Topic concerning the use of imaging techniques for clinical purposes for medical research. + VT 3.2.24 Radiology + The use of imaging techniques for clinical purposes for medical research. 1.4 + Radiology + VT 3.2.14 Nuclear medicine + Nuclear medicine + VT 3.2.13 Medical imaging @@ -49098,7 +49241,7 @@ positional features such as functional sites in nucleotide sequences. Light microscopy - Topic concerning the use of optical instruments to magnify the image of an object. + The use of optical instruments to magnify the image of an object. 1.4 @@ -49113,7 +49256,7 @@ positional features such as functional sites in nucleotide sequences.Laboratory animal science 1.4 - Topic concerning the use of animals and alternatives in experimental research. + The use of animals and alternatives in experimental research. @@ -49127,7 +49270,8 @@ positional features such as functional sites in nucleotide sequences.Marine biology 1.4 - Topic concerning the study of organisms in the ocean or brackish waters. + VT 1.5.18 Marine and Freshwater biology + The study of organisms in the ocean or brackish waters. @@ -49140,8 +49284,8 @@ positional features such as functional sites in nucleotide sequences. Molecular medicine + The identification of molecular and genetic causes of disease and the development of interventions to correct them. 1.4 - Topic concerning the identification of molecular and genetic causes of disease and the development of interventions to correct them. @@ -49154,8 +49298,10 @@ positional features such as functional sites in nucleotide sequences. Nutritional science - Topic concerning the study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices. 1.4 + VT 3.3.7 Nutrition and Dietetics + Dietetics + The study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices. Nutrition science @@ -49169,7 +49315,7 @@ positional features such as functional sites in nucleotide sequences. Omics - Topic concerning the collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. + The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. 1.4 @@ -49183,9 +49329,9 @@ positional features such as functional sites in nucleotide sequences. Quality affairs + The processes that need to be in place to ensure the quality of products for human or animal use. Good clinical practice Good manufacturing practice - Topic concerning the processes that need to be in place to ensure the quality of products for human or animal use. Quality assurance Good laboratory practice 1.4 @@ -49201,7 +49347,7 @@ positional features such as functional sites in nucleotide sequences. Regulatory affairs - Topic concerning the protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines. + The protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines. 1.4 @@ -49216,8 +49362,8 @@ positional features such as functional sites in nucleotide sequences.Regnerative medicine Stem cell research + Biomedical approaches to clinical interventions that involve the use of stem cells. 1.4 - Topic concerning biomedical approaches to clinical interventions that involve the use of stem cells. @@ -49231,7 +49377,7 @@ positional features such as functional sites in nucleotide sequences.Systems medicine 1.4 - Topic concerning an interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life. + An interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life. @@ -49259,8 +49405,8 @@ positional features such as functional sites in nucleotide sequences.Bioengineering 1.4 + The application of biological concepts and methods to the analytical and synthetic methodologies of engineering. Diagnostic markers - Topic concerning the application of biological concepts and methods to the analytical and synthetic methodologies of engineering. @@ -49273,9 +49419,11 @@ positional features such as functional sites in nucleotide sequences. Geriatric medicine + The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. + VT 3.2.10 Geriatrics and gerontology Ageing - Topic concerning the branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. Aging + Gerontology 1.4 Geriatrics @@ -49290,7 +49438,8 @@ positional features such as functional sites in nucleotide sequences. Allergy, clinical immunology and immunotherapeutics. - Topic concerning health issues related to the immune system and their prevention, diagnosis and mangement. + VT 3.2.1 Allergy + Health issues related to the immune system and their prevention, diagnosis and mangement. 1.4 Immune disorders Clinical immunology @@ -49309,10 +49458,10 @@ positional features such as functional sites in nucleotide sequences. Pain medicine - Topic concerning with the prevention of pain and the evaluation, treatment and rehabilitation of persons in pain. Ageing 1.4 Algiatry + The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain. @@ -49326,8 +49475,9 @@ positional features such as functional sites in nucleotide sequences.Anaesthesiology Anaesthetics + Anaesthesia and anaesthetics. 1.4 - Topic concerning anaesthesia and anaesthetics. + VT 3.2.2 Anaesthesiology @@ -49342,9 +49492,10 @@ positional features such as functional sites in nucleotide sequences. Acute medicine Geriatrics + VT 3.2.5 Critical care/Emergency medicine Emergency medicine 1.4 - Topic concerning the multidisciplinary that cares for patients with acute, life-threatening illness or injury. + The multidisciplinary that cares for patients with acute, life-threatening illness or injury. @@ -49357,9 +49508,10 @@ positional features such as functional sites in nucleotide sequences. Dermatology + The branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails. Dermatological disorders - Topic concerning the branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails. 1.4 + VT 3.2.7 Dermatology and venereal diseases @@ -49373,7 +49525,7 @@ positional features such as functional sites in nucleotide sequences.Dentistry 1.4 - Topic concerning the study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures. + The study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures. @@ -49386,11 +49538,13 @@ positional features such as functional sites in nucleotide sequences. Ear, nose and throat medicine - Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat. Otolaryngology 1.4 - Audiovestibular medicine + The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat. + Otorhinolaryngology Head and neck disorders + VT 3.2.20 Otorhinolaryngology + Audiovestibular medicine @@ -49406,8 +49560,8 @@ positional features such as functional sites in nucleotide sequences.1.4 Metabolic disorders Metabolism - Topic concerning the branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism. Endocrinology + The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism. Endocrine disorders @@ -49421,7 +49575,8 @@ positional features such as functional sites in nucleotide sequences. Haematology - Topic concerning the branch of medicine that deals with the blood, blood-forming organs and blood diseases. + VT 3.2.11 Hematology + The branch of medicine that deals with the blood, blood-forming organs and blood diseases. Haematological disorders 1.4 Blood disorders @@ -49437,9 +49592,10 @@ positional features such as functional sites in nucleotide sequences. Gastroenterology + The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum. Gastrointestinal disorders + VT 3.2.8 Gastroenterology and hepatology 1.4 - Topic concerning the branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum. @@ -49452,7 +49608,7 @@ positional features such as functional sites in nucleotide sequences. Gender medicine - Topic concerning the study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management. + The study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management. 1.4 @@ -49466,9 +49622,10 @@ positional features such as functional sites in nucleotide sequences. Gynaecology and obstetrics + VT 3.2.15 Obstetrics and gynaecology 1.4 - Topic concerning the branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. Gynaecology + The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. Gynaecological disorders Obstetrics @@ -49486,7 +49643,7 @@ positional features such as functional sites in nucleotide sequences.Hepatobiliary medicine Liver disorders 1.4 - Topic concerning the branch of medicine that deals with the liver, gallbladder, bile ducts and bile. + The branch of medicine that deals with the liver, gallbladder, bile ducts and bile. @@ -49499,8 +49656,8 @@ positional features such as functional sites in nucleotide sequences. Infectious tropical disease + The branch of medicine that deals with the infectious diseases of the tropics. 1.4 - Topic concerning the branch of medicine that deals with the infectious diseases of the tropics. @@ -49514,7 +49671,7 @@ positional features such as functional sites in nucleotide sequences.Trauma medicine 1.4 - Topic concerning the branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident. + The branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident. @@ -49527,7 +49684,7 @@ positional features such as functional sites in nucleotide sequences. Medical toxicology - Topic concerning the branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents. + The branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents. 1.4 @@ -49541,8 +49698,12 @@ positional features such as functional sites in nucleotide sequences. Musculoskeletal medicine - Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine. + The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine. + VT 3.2.26 Rheumatology + VT 3.2.19 Orthopaedics Musculoskeletal disorders + Orthopaedics + Rheumatology 1.4 @@ -49556,10 +49717,13 @@ positional features such as functional sites in nucleotide sequences. Opthalmology - 1.4 Eye disoders + VT 3.2.18 Optometry + 1.4 + Optometry + VT 3.2.17 Ophthalmology Audiovestibular medicine - Topic concerning the branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles. + The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles. @@ -49573,7 +49737,8 @@ positional features such as functional sites in nucleotide sequences.Paediatrics 1.4 - Topic concerning the branch of medicine that deals with the medical care of infants, children and adolescents. + The branch of medicine that deals with the medical care of infants, children and adolescents. + VT 3.2.21 Paediatrics Child health @@ -49587,9 +49752,10 @@ positional features such as functional sites in nucleotide sequences. Psychiatry + The branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour. 1.4 Psychiatric disorders - Topic concerning the branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour. + VT 3.2.23 Psychiatry Mental health @@ -49603,12 +49769,14 @@ positional features such as functional sites in nucleotide sequences. Reproductive health - Topic concerning the health of the reproductive processes, functions and systems at all stages of life. Reproductive disorders - Family planning Audiovestibular medicine - Fertility medicine + VT 3.2.3 Andrology + Andrology 1.4 + Family planning + The health of the reproductive processes, functions and systems at all stages of life. + Fertility medicine @@ -49621,7 +49789,9 @@ positional features such as functional sites in nucleotide sequences. Surgery - Topic concerning the use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance. + Transplantation + VT 3.2.28 Transplantation + The use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance. 1.4 @@ -49635,7 +49805,8 @@ positional features such as functional sites in nucleotide sequences. Urology and nephrology - Topic concerning the branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney. + The branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney. + VT 3.2.29 Urology and nephrology 1.4 Urology Kidney disease @@ -49653,10 +49824,12 @@ positional features such as functional sites in nucleotide sequences. Complementary medicine - Topic concerning medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health. + Medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health. + VT 3.2.12 Integrative and Complementary medicine Holistic medicine 1.4 Alternative medicine + Integrative medicine @@ -49670,10 +49843,10 @@ positional features such as functional sites in nucleotide sequences.MRI Nuclear magnetic resonance imaging - Topic concerning techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. 1.7 MRT Magnetic resonance tomography + Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. NMRI Magnetic resonance imaging @@ -49689,10 +49862,10 @@ positional features such as functional sites in nucleotide sequences.Neutron diffraction + The study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure. Neutron microscopy Elastic neutron scattering 1.7 - Topic concerning the study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure. Neutron diffraction experiment @@ -49706,8 +49879,8 @@ positional features such as functional sites in nucleotide sequences.Tomography X-ray tomography + Imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram). Electron tomography - Topic concerning imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram). 1.7 @@ -49721,9 +49894,10 @@ positional features such as functional sites in nucleotide sequences.Data mining 1.7 - Topic concerning the discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. - Knowledge Discovery in Databases - KDD + VT 1.3.2 Data mining + The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. + KDD + Knowledge discovery in databases @@ -49736,7 +49910,9 @@ positional features such as functional sites in nucleotide sequences.Machine learning A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an ouput, rather than relying on explicitly encoded information only. + Artificial Intelligence 1.7 + VT 1.2.2 Artificial Intelligence (expert systems, machine learning, robotics) @@ -49746,10 +49922,16 @@ positional features such as functional sites in nucleotide sequences. - Biological databases + Database management 1.8 - Topic concerning databases of biological information including the results of scientific experiments, the application of high-throughput technology, computational analysis and the the scientific literature. + Data maintenance + Databases + Database administration + The general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. + + This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature. + Biological databases @@ -49761,13 +49943,14 @@ positional features such as functional sites in nucleotide sequences. Animals - The resource may be specific to a plant, a group of plants or all plants. 1.8 Animal biology + Animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation. Zoology Animal + VT 1.5.29 Zoology + The resource may be specific to a plant, a group of plants or all plants. Metazoa - Topic concerning animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation. @@ -49779,10 +49962,10 @@ positional features such as functional sites in nucleotide sequences. Protein sites, features and motifs - Topic concerning the biologiy, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. Protein sequence features Protein functional sites 1.8 + The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. @@ -49797,7 +49980,7 @@ positional features such as functional sites in nucleotide sequences.Nucleic acid sequence features 1.8 Nucleic acid functional sites - Topic concerning the biologiy, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. + The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. @@ -49810,8 +49993,8 @@ positional features such as functional sites in nucleotide sequences.Gene transcript features - Topic concerning features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. Nucleic acid features (mRNA features) + Features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. mRNA features This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). 1.8 @@ -49826,8 +50009,8 @@ positional features such as functional sites in nucleotide sequences. Protein-ligand interactions - Topic concerning protein-ligand (small molecule) interaction(s). 1.8 + Protein-ligand (small molecule) interaction(s). @@ -49839,8 +50022,8 @@ positional features such as functional sites in nucleotide sequences. Protein-drug interactions - Topic concerning protein-drug interaction(s). 1.8 + Protein-drug interaction(s). @@ -49853,7 +50036,7 @@ positional features such as functional sites in nucleotide sequences.Genotyping experiment 1.8 - Topic concerning genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. + Genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. @@ -49866,8 +50049,8 @@ positional features such as functional sites in nucleotide sequences.GWAS study 1.8 + Genome-wide association study experiments. Genome-wide association study - Topic concerning genome-wide association study experiments. @@ -49879,9 +50062,9 @@ positional features such as functional sites in nucleotide sequences. Microarray experiment - Topic concerning microarray experiments including conditions, protocol, sample:data relationships etc. 1.8 This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. + Microarray experiments including conditions, protocol, sample:data relationships etc. @@ -49894,7 +50077,7 @@ positional features such as functional sites in nucleotide sequences.PCR experiment 1.8 - Topic concerning PCR experiments, e.g. quantitative real-time PCR. + PCR experiments, e.g. quantitative real-time PCR. @@ -49906,8 +50089,8 @@ positional features such as functional sites in nucleotide sequences. Proteomics experiment + Proteomics experiments. 1.8 - Topic concerning proteomics experiments. @@ -49919,7 +50102,7 @@ positional features such as functional sites in nucleotide sequences. 2D PAGE experiment - Topic concerning two-dimensional gel electrophoresis experiments, gels or spots in a gel. + Two-dimensional gel electrophoresis experiments, gels or spots in a gel. 1.8 @@ -49932,7 +50115,7 @@ positional features such as functional sites in nucleotide sequences. Northern blot experiment - Topic concerning Northern Blot experiments. + Northern Blot experiments. 1.8 @@ -49946,7 +50129,7 @@ positional features such as functional sites in nucleotide sequences.RNAi experiment 1.8 - Topic concerning RNAi experiments. + RNAi experiments. @@ -49959,7 +50142,7 @@ positional features such as functional sites in nucleotide sequences.Simulation experiment 1.8 - Topic concerning biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. + Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. @@ -49972,7 +50155,7 @@ positional features such as functional sites in nucleotide sequences.Protein-nucleic acid interactions 1.8 - Topic concerning protein-DNA/RNA interaction(s). + Protein-DNA/RNA interaction(s). @@ -49984,8 +50167,8 @@ positional features such as functional sites in nucleotide sequences. Protein-protein interactions - Topic concerning protein-protein interaction(s), including interactions between protein domains. Domain-domain interactions + Protein-protein interaction(s), including interactions between protein domains. 1.8 Protein interaction networks @@ -50000,7 +50183,7 @@ positional features such as functional sites in nucleotide sequences.Cellular process pathways 1.8 - Topic concernning cellular process pathways. + Cellular process pathways. @@ -50012,7 +50195,7 @@ positional features such as functional sites in nucleotide sequences. Disease pathways - Topic concerning disease pathways, typically of human disease. + Disease pathways, typically of human disease. Pathway or network (disease) 1.8 @@ -50026,7 +50209,7 @@ positional features such as functional sites in nucleotide sequences. Environmental information processing pathways - Topic concerning environmental information processing pathways. + Environmental information processing pathways. 1.8 Pathway or network (environmental information processing) @@ -50040,9 +50223,9 @@ positional features such as functional sites in nucleotide sequences. Genetic information processing pathways - Topic concerning genetic information processing pathways. Pathway or network (genetic information processing) 1.8 + Genetic information processing pathways. @@ -50054,10 +50237,10 @@ positional features such as functional sites in nucleotide sequences. Protein super-secondary structure + Super-secondary structure of protein sequence(s). Protein features (super-secondary) 1.8 Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. - Topic concerning super-secondary structure of protein sequence(s). @@ -50071,8 +50254,8 @@ positional features such as functional sites in nucleotide sequences. Enzyme active site 1.8 - Topic concerning catalytic residues (active site) of an enzyme. Protein features (active sites) + Catalytic residues (active site) of an enzyme. @@ -50084,8 +50267,8 @@ positional features such as functional sites in nucleotide sequences. Protein binding sites + Ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. 1.8 - Topic concerning ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. Protein features (binding sites) @@ -50098,7 +50281,7 @@ positional features such as functional sites in nucleotide sequences. Protein-nucleic acid binding sites - Topic concerning RNA and DNA-binding proteins and binding sites in protein sequences. + RNA and DNA-binding proteins and binding sites in protein sequences. 1.8 Protein features (nucleic acid binding sites) @@ -50112,7 +50295,7 @@ positional features such as functional sites in nucleotide sequences. Protein cleavage sites - Topic concerning cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. + Cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. Protein features (cleavage sites) 1.8 @@ -50126,7 +50309,7 @@ positional features such as functional sites in nucleotide sequences. Protein chemical modifications - Topic concerning chemical modification of a protein. + Chemical modification of a protein. Protein features (chemical modifications) MOD:00000 1.8 @@ -50142,7 +50325,7 @@ positional features such as functional sites in nucleotide sequences. Protein disordered structure - Topic concerning disordered structure in a protein. + Disordered structure in a protein. 1.8 Protein features (disordered structure) @@ -50158,8 +50341,8 @@ positional features such as functional sites in nucleotide sequences. The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. + Structural domains or 3D folds in a protein or polypeptide chain. 1.8 - Topic concerning structural domains or 3D folds in a protein or polypeptide chain. Protein structural domains Protein features (domains) @@ -50176,7 +50359,7 @@ positional features such as functional sites in nucleotide sequences. Protein features (key folding sites) 1.8 - Topic concerning key residues involved in protein folding. + Key residues involved in protein folding. @@ -50190,7 +50373,7 @@ positional features such as functional sites in nucleotide sequences. Protein features (post-translation modifications) Post-translation modifications - Topic concerning post-translation modifications in a protein sequence, typically describing the specific sites involved. + Post-translation modifications in a protein sequence, typically describing the specific sites involved. 1.8 @@ -50205,8 +50388,8 @@ positional features such as functional sites in nucleotide sequences. The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). + Secondary structure (predicted or real) of a protein. Protein features (secondary structure) - Topic concerning secondary structure (predicted or real) of a protein. 1.8 @@ -50220,8 +50403,8 @@ positional features such as functional sites in nucleotide sequences.Protein sequence repeats 1.8 - Topic concerning short repetitive subsequences (repeat sequences) in a protein sequence. Protein features (repeats) + Short repetitive subsequences (repeat sequences) in a protein sequence. Protein repeats @@ -50235,14 +50418,156 @@ positional features such as functional sites in nucleotide sequences.Protein signal peptides Protein features (signal peptides) + Signal peptides or signal peptide cleavage sites in protein sequences. 1.8 - Topic concerning signal peptides or signal peptide cleavage sites in protein sequences. + + + + Applied mathematics + + VT 1.1.1 Applied mathematics + The application of mathematics to specific problems in science, typically by the formulation and analysis of mathematical models. + 1.10 + + + + + + + + + + Pure mathematics + + VT 1.1.1 Pure mathematics + The study of abstract mathematical concepts. + 1.10 + + + + + + + + + + Data governance + + Data handling + http://purl.bioontology.org/ontology/MSH/D030541 + The control of data entry and maintenance to ensure the data meets defined standards, qualities or constraints. + 1.10 + Data stewardship + + + + + + + + + + Data quality management + + http://purl.bioontology.org/ontology/MSH/D030541 + 1.10 + Data quality + Data integrity + Data clean-up + Data enrichment + The quality, integrity, cleaning up and enrichment of data. + + + + + + + + + + Freshwater biology + + 1.10 + VT 1.5.18 Marine and Freshwater biology + The study of organisms in freshwater ecosystems. + + + + + + + + + + + Human genetics + + The study of inheritatnce in human beings. + VT 3.1.2 Human genetics + 1.10 + + + + + + + + + + + Tropical medicine + + 1.10 + Health problems that are prevalent in tropical and subtropical regions. + VT 3.3.14 Tropical medicine + + + + + + + + + + + Medical biotechnology + + 1.10 + VT 3.4.1 Biomedical devices + VT 3.4.2 Health-related biotechnology + VT 3.4 Medical biotechnology + VT 3.3.14 Tropical medicine + Pharmaceutical biotechnology + Biotechnology applied to the medical sciences and the development of medicines. + + + + + + + + + + + Personalized medicine + + 1.10 + Health problems that are prevalent in tropical and subtropical regions. + Molecular diagnostics + VT 3.4.5 Molecular diagnostics + + + + + + +