diff --git a/releases/EDAM.owl b/releases/EDAM.owl index 4941ab6..b0b3ee1 100644 --- a/releases/EDAM.owl +++ b/releases/EDAM.owl @@ -29,28 +29,28 @@ xmlns:edam="&oboOther;edam#"> EDAM_topic http://edamontology.org/topic_ "EDAM topics" - 08:02:2016 22:15GMT EDAM_operation http://edamontology.org/operation_ "EDAM operations" formats "EDAM data formats" EDAM - An ontology of bioinformatics topics, operations, types of data including identifiers, and data formats Jon Ison, Matus Kalas, Hervé Ménager identifiers "EDAM types of identifiers" data "EDAM types of data" relations "EDAM relations" 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. - 3702 operations "EDAM operations" + Bioinformatics operations, data types, formats, identifiers and topics EDAM http://edamontology.org/ "EDAM relations and concept properties" application/rdf+xml EDAM_data http://edamontology.org/data_ "EDAM types of data" concept_properties "EDAM concept properties" Jon Ison + 3730 Matúš Kalaš EDAM_format http://edamontology.org/format_ "EDAM data formats" - 1.13 + 1.14 topics "EDAM topics" + 24:02:2016 21:54GMT Hervé Ménager 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. @@ -418,8 +418,8 @@ - true In very unusual cases. + true @@ -465,14 +465,14 @@ - In very unusual cases. true + In very unusual cases. - OBO_REL:has_participant 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. + OBO_REL:has_participant @@ -505,8 +505,8 @@ - In very unusual cases. true + In very unusual cases. @@ -541,8 +541,8 @@ - In very unusual cases. true + In very unusual cases. @@ -569,8 +569,8 @@ - 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. + OBO_REL:quality_of @@ -598,20 +598,20 @@ - true In very unusual cases. + true - 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 + 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. - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. OBO_REL:inheres_in + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. @@ -694,16 +694,16 @@ - In very unusual cases. - true + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. + OBO_REL:participates_in - + - OBO_REL:participates_in - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. + In very unusual cases. + true - + @@ -741,8 +741,8 @@ - true In very unusual cases. + true @@ -800,20 +800,20 @@ - 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). + Data record EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - Data set + Datum EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - Datum + Data set @@ -1235,8 +1235,8 @@ beta12orEarlier This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on. Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element. - - + + @@ -1959,7 +1959,7 @@ - + beta12orEarlier @@ -2022,6 +2022,7 @@ The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. Nucleic acid physicochemical property beta12orEarlier + GC-content @@ -2190,8 +2191,8 @@ - Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. SO:0001248 + Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. @@ -2324,11 +2325,13 @@ Sequence tag profile (with gene assignment) - + + 1.14 beta12orEarlier + true Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers. - - + + @@ -4548,13 +4551,13 @@ - + - + Unique name of a codon usage table. @@ -5995,8 +5998,8 @@ - UniProt|Enzyme Nomenclature A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. + UniProt|Enzyme Nomenclature @@ -6530,7 +6533,7 @@ - + A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information. @@ -10761,7 +10764,7 @@ CDF file beta12orEarlier beta12orEarlier - + @@ -10777,7 +10780,7 @@ GIN file beta12orEarlier beta12orEarlier - + @@ -17025,6 +17028,8 @@ SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from. beta12orEarlier Sequencing-based expression profile + This includes tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers. + Sequence tag profile (with gene assignment) Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed. @@ -19185,8 +19190,9 @@ + General annotation on an oligonucleotide probe, or a set of probes. beta12orEarlier - General annotation on an oligonucleotide probe. + Oligonucleotide probe sets annotation @@ -21614,11 +21620,13 @@ Oligonucleotide probe sets annotation - + beta12orEarlier + 1.14 + true General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set. - - + + @@ -23743,6 +23751,149 @@ + + + + Biodiversity report + + Biodiversity information + 1.9 + A report about biodiversity data. + + + + + + + + + + Biosafety report + + A report about biosafety data. + Biosafety information + 1.14 + + + + + + + + + + Isolation report + + Geographic location + Isolation source + 1.14 + A report about any kind of isolation of biological material. + + + + + + + + + + Pathogenicity report + + 1.14 + Information about the ability of an organism to cause disease in a corresponding host. + Pathogenicity + + + + + + + + + + Biosafety classification + + Information about the biosafety classification of an organism according to corresponding law. + Biosafety level + 1.14 + + + + + + + + + + Geographic location + + A report about localisation of the isolaton of biological material e.g. country or coordinates. + 1.14 + + + + + + + + + + Isolation source + + A report about any kind of isolation source of biological material e.g. blood, water, soil. + 1.14 + + + + + + + + + + Physiology parameter + + Experimentally determined parameter of the physiology of an organism, e.g. substrate spectrum. + 1.14 + + + + + + + + + + Morphology parameter + + Experimentally determined parameter of the morphology of an organism, e.g. size & shape. + 1.14 + + + + + + + + + + Cultivation parameter + + Salinity + Carbon source + Experimental determined parameter for the cultivation of an organism. + Cultivation conditions + Temperature + 1.14 + Culture media composition + pH value + Nitrogen source + + + + + + @@ -26375,17 +26526,17 @@ - File format - File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. - - - - Data model A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) + + File format + File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + + + @@ -26803,11 +26954,11 @@ - MSF + GCG MSF - GCG MSF beta12orEarlier GCG MSF (multiple sequence file) file format. + MSF @@ -28100,7 +28251,7 @@ - + beta12orEarlier @@ -32638,6 +32789,233 @@ experiments employing a combination of technologies. + + + + MSF + + Magellan storage file format + This format corresponds to an SQLite database, and you can look into the files with e.g. SQLiteStudio3. There are also some readers (http://pubs.acs.org/doi/abs/10.1021/pr2005154) and converters (http://www.sciencedirect.com/science/article/pii/S1874391915300531) for this format available, which re-engineered the database schema, but there is no official DB schema specification of Thermo Scientific for the format. + Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer software. + 1.14 + + + + + + + + + + Biodiversity data format + + + + + + + + Data format for biodiversity data. + 1.14 + + + + + + + + + + ABCD format + + + + + + + + ABCD + Exchange format of the Access to Biological Collections Data (ABCD) Schema; a standard for the access to and exchange of data about specimens and observations (primary biodiversity data). + 1.14 + + + + + + + + + + + GCT/Res format + + + Res format + Tab-delimited text files of GenePattern that contain a column for each sample, a row for each gene, and an expression value for each gene in each sample. + GCT format + 1.14 + + + + + + + + + + WIFF format + + + wiff + wiff + 1.14 + Mass spectrum file format from QSTAR and QTRAP instruments (ABI/Sciex). + + + + + + + + + + X!Tandem XML + + + + Output format used by X! series search engines that is based on the XML language BIOML. + 1.14 + + + + + + + + + + + Thermo RAW + + + Proprietary format for which documentation is not available. + Proprietary file format for mass spectrometry data from Thermo Scientific. + 1.14 + + + + + + + + + + Mascot .dat file + + + "Raw" result file from Mascot database search. + 1.14 + + + + + + + + + + + MaxQuant APL peaklist format + + + 1.14 + MaxQuant APL + Format of peak list files from Andromeda search engine (MaxQuant) that consist of arbitrarily many spectra. + + + + + + + + + + + SBOL + + 1.14 + SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. + Synthetic Biology Open Language (SBOL) is an XML format for the specification and exchange of biological design information in synthetic biology. + + + + + + + + + + + PMML + + One or more mining models can be contained in a PMML document. + 1.14 + PMML uses XML to represent mining models. The structure of the models is described by an XML Schema. + + + + + + + + + + + OME-TIFF + + + Image file format used by the Open Microscopy Environment (OME). + + 1.14 + OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data. It is a joint project between universities, research establishments, industry and the software development community. + An OME-TIFF dataset consists of one or more files in standard TIFF or BigTIFF format, with the file extension .ome.tif or .ome.tiff, and an identical (or in the case of multiple files, nearly identical) string of OME-XML metadata embedded in the ImageDescription tag of each file’s first IFD (Image File Directory). BigTIFF file extensions are also permitted, with the file extension .ome.tf2, .ome.tf8 or .ome.btf, but note these file extensions are an addition to the original specification, and software using an older version of the specification may not be able to handle these file extensions. + + + + + + + + + + + LocARNA PP + + 1.14 + Format for multiple aligned or single sequences together with the probabilistic description of the (consensus) RNA secondary structure ensemble by probabilities of base pairs, base pair stackings, and base pairs and unpaired bases in the loop of base pairs. + The LocARNA PP format combines sequence or alignment information and (respectively, single or consensus) ensemble probabilities into an PP 2.0 record. + + + + + + + + + + + dbGaP format + + Input format used by the Database of Genotypes and Phenotypes (dbGaP). + The Database of Genotypes and Phenotypes (dbGaP) is a National Institutes of Health (NIH) sponsored repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype. + 1.14 + + + + + + + @@ -32681,8 +33059,8 @@ experiments employing a combination of technologies. - Process Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. + Process @@ -32708,14 +33086,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -32750,14 +33128,14 @@ experiments employing a combination of technologies. - - + + - - + + Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. @@ -32884,14 +33262,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -32935,14 +33313,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33009,14 +33387,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33197,7 +33575,6 @@ experiments employing a combination of technologies. Residue interaction calculation - @@ -33303,14 +33680,14 @@ experiments employing a combination of technologies. - - + + - - + + Sequence feature prediction @@ -33363,20 +33740,20 @@ experiments employing a combination of technologies. - - + + - + - - + + beta12orEarlier @@ -33621,14 +33998,14 @@ experiments employing a combination of technologies. - - + + - - + + Predict tertiary structure of a molecular (biopolymer) sequence. @@ -33667,14 +34044,14 @@ experiments employing a combination of technologies. - - + + - - + + Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. @@ -33723,14 +34100,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33928,20 +34305,14 @@ experiments employing a combination of technologies. - - - - - - - + - + @@ -33953,6 +34324,12 @@ experiments employing a combination of technologies. + + + + + + @@ -33974,14 +34351,14 @@ experiments employing a combination of technologies. - - + + - - + + Identify and plot third base position variability in a nucleotide sequence. @@ -34013,14 +34390,14 @@ experiments employing a combination of technologies. - - + + - - + + Sequence distance matrix construction @@ -34167,20 +34544,20 @@ experiments employing a combination of technologies. - - + + - - + + - - + + Sequence profile construction @@ -34200,20 +34577,20 @@ experiments employing a combination of technologies. - - + + - - + + - + Structural profile generation @@ -34239,14 +34616,14 @@ experiments employing a combination of technologies. - - + + - - + + Sequence profile alignment @@ -34300,12 +34677,6 @@ experiments employing a combination of technologies. - - - - - - @@ -34316,6 +34687,12 @@ experiments employing a combination of technologies. + + + + + + Sequence-profile alignment construction Sequence-profile alignment generation beta12orEarlier @@ -34336,14 +34713,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34366,14 +34743,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34510,8 +34887,8 @@ experiments employing a combination of technologies. - - + + @@ -34522,8 +34899,8 @@ experiments employing a combination of technologies. - - + + This includes predicting primers based on gene structure, promoters, exon-exon junctions, predicting primers that are conserved across multiple genomes or species, primers for for gene transcription profiling, for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs), for large scale sequencing, or for methylation PCRs. @@ -34564,13 +34941,13 @@ experiments employing a combination of technologies. - + - + Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. @@ -34590,14 +34967,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34617,13 +34994,13 @@ experiments employing a combination of technologies. - + - + @@ -34770,13 +35147,13 @@ experiments employing a combination of technologies. - + - + beta12orEarlier @@ -34871,14 +35248,14 @@ experiments employing a combination of technologies. - - + + - - + + Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. @@ -34933,13 +35310,13 @@ experiments employing a combination of technologies. - + - + @@ -35022,13 +35399,13 @@ experiments employing a combination of technologies. - + - + Protein SNP mapping @@ -35065,14 +35442,14 @@ experiments employing a combination of technologies. - - + + - - + + Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). @@ -35147,8 +35524,8 @@ experiments employing a combination of technologies. - - + + @@ -35159,8 +35536,8 @@ experiments employing a combination of technologies. - - + + Visualization @@ -35456,11 +35833,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry. 1.6 - Protein fingerprinting true beta12orEarlier - Peptide mass fingerprinting - + @@ -36137,14 +36512,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Calculate pH-dependent properties from pKa calculations of a protein sequence. @@ -37908,14 +38283,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + RNA secondary structure alignment generation @@ -38332,12 +38707,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Tag mapping - - - - - - Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. Tag to gene assignment Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts. @@ -38589,14 +38958,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Phylogenetic tree construction (from gene frequencies) @@ -38777,14 +39146,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict families of genes and gene function based on their position in a phylogenetic tree. @@ -38986,14 +39355,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Sequence alignment rendering @@ -39095,14 +39464,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Structure rendering @@ -40328,14 +40697,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Structure analysis (protein) @@ -40380,7 +40749,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - File handling + Data handling @@ -40388,12 +40757,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Basic (non-analytical) operations of some data, either a file or equivalent entity in memory. - File processing beta12orEarlier + File processing Report handling - Data handling + File handling Utility operation + Processing + Basic (non-analytical) operations of some data, either a file or equivalent entity in memory, such that the same basic type of data is consumed as input and generated as output. @@ -40836,14 +41206,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict a network of gene regulation. @@ -41040,14 +41410,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Compare two or more molecular sequences. @@ -41095,14 +41465,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Gene component prediction @@ -41244,14 +41614,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Identify or predict protein-protein interactions, interfaces, binding sites etc. @@ -41447,14 +41817,14 @@ 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. @@ -41473,14 +41843,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). @@ -41540,14 +41910,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse nucleic acid tertiary structural data. @@ -41733,14 +42103,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict the interactions of proteins with other molecules. @@ -42192,14 +42562,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -42233,14 +42603,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -42324,8 +42694,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein fragment weight comparison + Calculate the molecular weight of a protein (or fragments) and compare it to another protein or reference data. Generally used for protein identification. + Peptide mass fingerprinting + Protein fingerprinting beta12orEarlier - Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data. + PMF @@ -42535,14 +42908,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -42558,8 +42931,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Analysis - Process or apply analytical methods to existing data of a specific type. - Processing + Apply analytical methods to existing data of a specific type. + This excludes non-analytical methods that read and write the same basic type of data (for that, see 'Data handling'). beta12orEarlier @@ -43052,14 +43425,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta13 @@ -43088,7 +43461,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Editing - + beta13 Edit a data entity, either randomly or specifically. @@ -43105,8 +43478,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + @@ -43117,8 +43490,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + Assembly quality evaluation @@ -43940,14 +44313,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + Infer a transcriptome sequence by analysis of short sequence reads. @@ -44121,14 +44494,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + Generate a checksum of a molecular sequence. @@ -44231,14 +44604,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + Recognition of which format the given data is in. @@ -44253,8 +44626,8 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs. - + @@ -45110,20 +45483,20 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + - - + + 1.12 @@ -45250,9 +45623,8 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - Peptide-spectrum-matching - Predict the isotope distribution of a given chemical species. 1.12 + Calculate the isotope distribution of a given chemical species. @@ -45262,8 +45634,9 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - Retention times calculation + Retention times prediction + Retention times calculation Prediction of retention times in a mass spectrometry experiment based on compositional and structural properties of the separated species. 1.12 @@ -45683,6 +46056,63 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp + + + + Reference identification + + Identification of the best reference for mapping for a specific dataset from a list of potential references, when performing genetic variation analysis. + 1.1 + + + + + + + + + + Ion counting + + Ion current integration + Label-free quantification by integration of ion current (ion counting). + 1.14 + + + + + + + + + + Isotope-coded protein label + + Chemical tagging free amino groups of intact proteins with stable isotopes. + ICPL + 1.14 + + + + + + + + + + Metabolic labeling + + Labeling all proteins and (possibly) all amino acids using C-13 or N-15 enriched grown medium or feed. + 1.14 + This includes N-15 metabolic labeling (labeling all proteins and (possibly) all amino acids using N-15 enriched grown medium or feed) and C-13 metabolic labeling (labeling all proteins and (possibly) all amino acids using C-13 enriched grown medium or feed). + N-15 metabolic labeling + C-13 metabolic labeling + + + + + + @@ -47259,7 +47689,7 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated true beta12orEarlier primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc. - + @@ -47585,15 +48015,19 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated - Gene families + Gene and protein families + beta12orEarlier - Gene family - Gene system - Gene and protein families - Particular gene(s), gene family or other gene group or system and their encoded proteins. + Gene family + A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. + Protein families Genes, gene family or system + Gene system + Protein sequence classification + Particular gene(s), gene family or other gene group or system and their encoded proteins.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. true + Gene families @@ -47695,7 +48129,7 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated true Specific protein beta12orEarlier - + @@ -47947,16 +48381,13 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated Protein families - - true + 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. + true 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. - - - + 1.14 + + @@ -48053,13 +48484,13 @@ positional features such as functional sites in nucleotide sequences. Transcription factors and regulatory sites + - CpG islands 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. - Attenuators Enhancers + Attenuators CAAT signals Transcriptional regulatory sites TFBS @@ -48382,7 +48813,7 @@ 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. true beta12orEarlier @@ -48399,7 +48830,7 @@ 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 Enzymology @@ -49189,7 +49620,7 @@ positional features such as functional sites in nucleotide sequences. Immunoproteins, genes and antigens - + Immunopeptides Immunity-related genes, proteins and their ligands. @@ -50446,7 +50877,7 @@ 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. + Topic concerning the the patterns, cause, and effect of disease within populations. true 1.3 Public health @@ -51401,8 +51832,8 @@ positional features such as functional sites in nucleotide sequences. Veterinary medicine + Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals. 1.4 - Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals. @@ -52075,7 +52506,7 @@ positional features such as functional sites in nucleotide sequences.1.8 true Protein-drug interaction(s). - +