From 6d44a264a72f78e3040831c65a33b245581ec669 Mon Sep 17 00:00:00 2001 From: matuskalas Date: Tue, 1 Nov 2016 03:48:41 +0100 Subject: [PATCH] History of releases: 1.12 --- releases/EDAM.owl | 2907 ++++++++++++++++++++++++++++++++++------------------- 1 file changed, 1899 insertions(+), 1008 deletions(-) diff --git a/releases/EDAM.owl b/releases/EDAM.owl index 145874d..10f0fe5 100644 --- a/releases/EDAM.owl +++ b/releases/EDAM.owl @@ -30,13 +30,14 @@ EDAM_topic http://edamontology.org/topic_ "EDAM topics" EDAM_operation http://edamontology.org/operation_ "EDAM operations" - 09:07:2015 - 3625 + 18:12:2015 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" + 3680 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. @@ -47,11 +48,10 @@ concept_properties "EDAM concept properties" Jon Ison Matúš Kalaš - Jon Ison, Matus Kalas, Hervé Ménager EDAM_format http://edamontology.org/format_ "EDAM data formats" topics "EDAM topics" - 1.11 Hervé Ménager + 1.12 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. @@ -362,17 +362,17 @@ - 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 + + In very unusual cases. + true + + + @@ -415,16 +415,16 @@ - 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. + In very unusual cases. + true - + - true - In very unusual cases. + '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 - + @@ -519,8 +519,8 @@ - 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 @@ -548,8 +548,8 @@ - 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. + OBO_REL:inheres_in @@ -560,8 +560,8 @@ - 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 @@ -609,14 +609,14 @@ - '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' 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. - In very unusual cases. true + In very unusual cases. @@ -644,14 +644,14 @@ - In very unusual cases. true + In very unusual cases. - 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 @@ -685,16 +685,16 @@ - 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. - + - In very unusual cases. - true + 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 - + @@ -708,7 +708,6 @@ --> - @@ -750,20 +749,20 @@ - Data set EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Data set - Datum EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Datum - 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 @@ -802,7 +801,7 @@ Ontology - + @@ -1300,10 +1299,11 @@ - Sequence profile alignment + Profile-profile alignment beta12orEarlier A profile-profile alignment (each profile typically representing a sequence alignment). + Sequence profile alignment @@ -1359,7 +1359,7 @@ Phylogenetic tree - + @@ -1875,17 +1875,23 @@ Protein interaction report - + - beta12orEarlier Protein report (interaction) + beta12orEarlier Protein interaction record - An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with some other molecule(s), which might be another protein, nucleic acid or some other ligand. + Residue interaction data + Atom interaction data + Protein non-covalent interactions report + An informative report on interactions (predicted or known) within or between a protein, structural domain or part of a protein. This includes intra- and inter-residue contacts and distances, as well as interactions with other proteins and non-protein entities such as nucleic acid, metal atoms, water, ions etc. + + + @@ -2128,6 +2134,7 @@ beta12orEarlier An assembly of fragments of a (typically genomic) DNA sequence. + Contigs http://en.wikipedia.org/wiki/Sequence_assembly SO:0001248 Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included. @@ -2410,8 +2417,10 @@ Peak list Protein fingerprint + A molecular weight standard fingerprint is standard protonated molecular masses e.g. from trypsin (modified porcine trypsin, Promega) and keratin peptides. A set of peptide masses (peptide mass fingerprint) from mass spectrometry. beta12orEarlier + Molecular weights standard fingerprint @@ -2683,7 +2692,6 @@ Small molecule annotation - Small molecule report Chemical structure report An informative report on a specific chemical compound. beta12orEarlier @@ -2797,7 +2805,7 @@ Article - + @@ -4493,13 +4501,13 @@ - + - + Unique name of a codon usage table. @@ -4711,7 +4719,6 @@ A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. beta12orEarlier - Ontology concept ID @@ -5680,15 +5687,9 @@ Disease ID - - - - - - - - Identifier of an entry from a database of disease. + + Accession number of an entry from a database of disease. beta12orEarlier @@ -6482,12 +6483,6 @@ - - - - - - @@ -6999,7 +6994,7 @@ Map - + @@ -8250,12 +8245,14 @@ Sequence alignment (nucleic acid pair) - - + beta12orEarlier Alignment of exactly two nucleotide sequences. - - + true + 1.12 + + + @@ -8264,12 +8261,14 @@ Sequence alignment (protein pair) - - + + true + 1.12 Alignment of exactly two protein sequences. beta12orEarlier - - + + + @@ -8760,13 +8759,12 @@ Phylogenetic report + Phylogenetic tree-derived report + This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis. beta12orEarlier A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. Phylogenetic tree report 1.5 - Phylogenetic report - Phylogenetic tree-derived report - This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis. true @@ -9065,13 +9063,13 @@ - + - + beta12orEarlier @@ -9333,13 +9331,15 @@ Structure alignment (protein pair) - - + + 1.12 Protein pair structural alignment + true beta12orEarlier Alignment (superimposition) of exactly two protein tertiary (3D) structures. - - + + + @@ -9457,13 +9457,15 @@ Structure alignment (nucleic acid pair) - - + beta12orEarlier + 1.12 + true Nucleic acid pair structure alignment Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. - - + + + @@ -9491,8 +9493,7 @@ RNA structure alignment Alignment (superimposition) of RNA tertiary (3D) structures. beta12orEarlier - - + @@ -9689,7 +9690,6 @@ 1.5 Protein report (enzyme) beta12orEarlier - Enzyme report An informative report on a specific enzyme. @@ -9703,13 +9703,12 @@ Restriction enzyme report An informative report on a specific restriction enzyme such as enzyme reference data. - Restriction enzyme pattern data - beta12orEarlier - 1.5 This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. + Restriction enzyme pattern data Protein report (restriction enzyme) - Restriction enzyme report + beta12orEarlier true + 1.5 @@ -9963,7 +9962,7 @@ Protein structure-derived report This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure). Protein property (structural) - Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains. + Annotation about, or structural information derived from, one or more specific protein 3D structure(s) or structural domains. beta12orEarlier Protein report (structure) Protein structure report (domain) @@ -9994,20 +9993,14 @@ - Protein residue interactions - - - - - - - - Residue interaction data + Protein non-covalent interactions report + Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups. beta12orEarlier - Atom interaction data - - + true + 1.12 + + @@ -10034,8 +10027,8 @@ - Protein solvent accessibility - + Protein solvent accessibility report + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. beta12orEarlier Data on the solvent accessible or buried surface area of a protein structure. @@ -10092,7 +10085,8 @@ Protein distance matrix - + + beta12orEarlier A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. @@ -10105,7 +10099,7 @@ Protein contact map - + An amino acid residue contact map for a protein structure. beta12orEarlier @@ -10118,7 +10112,7 @@ Protein residue 3D cluster - + beta12orEarlier Report on clusters of contacting residues in protein structures such as a key structural residue network. @@ -10131,7 +10125,7 @@ Protein hydrogen bonds - + Patterns of hydrogen bonding in protein structures. beta12orEarlier @@ -10329,6 +10323,7 @@ Protein-ligand interaction report + Protein-drug interaction report beta12orEarlier An informative report on protein-ligand (small molecule) interaction(s). @@ -10546,7 +10541,6 @@ Nucleic acid report (folding model) RNA secondary structure folding probablities A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc. - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. RNA secondary structure folding classification @@ -10558,7 +10552,7 @@ Codon usage table - + @@ -10674,7 +10668,6 @@ An informative report on a specific disease. For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. beta12orEarlier - Disease report @@ -10747,11 +10740,13 @@ Molecular weights standard fingerprint - + beta12orEarlier + true + 1.12 Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS. - - + + @@ -13416,8 +13411,9 @@ Map attribute + A molecular map (genetic or physical), an attribute of such a map, or data extracted from or derived from the analysis of such a map. beta12orEarlier - An attribute of a molecular map (genetic or physical), or data extracted from or derived from the analysis of such a map. + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. @@ -13614,7 +13610,7 @@ 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 @@ -14131,13 +14127,13 @@ - + - + Identifier of a codon usage table, for example a genetic code. @@ -14692,7 +14688,6 @@ Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. beta12orEarlier Sequence conservation report - Sequence similarity plot A plot of sequence similarities identified from word-matching or character comparison. @@ -15896,7 +15891,7 @@ Resource metadata - + Data concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing. This is a broad data type and is used a placeholder for other, more specific types. Provenance metadata @@ -16241,7 +16236,6 @@ beta12orEarlier true Data concerning two-dimensional polygel electrophoresis. - @@ -16773,13 +16767,13 @@ Protein-drug interaction report - - - + + true An informative report on tentative or known protein-drug interaction(s). + 1.12 beta12orEarlier - - + + @@ -16807,7 +16801,6 @@ Phylogenetic data Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. - Phylogenetic data This is a broad data type and is used a placeholder for other, more specific types. beta12orEarlier @@ -18247,7 +18240,6 @@ Cell type identifier beta12orEarlier - Cell type ID A unique identifier of a type or group of cells. @@ -18355,13 +18347,13 @@ - + - + beta12orEarlier @@ -19851,11 +19843,13 @@ Identifier with metadata - + Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance. beta12orEarlier - - + true + 1.12 + + @@ -20414,13 +20408,13 @@ - + - + Identifier of a lipid. @@ -20926,7 +20920,6 @@ A protein sequence and associated metadata. beta12orEarlier - Protein sequence record Sequence record (protein) @@ -21018,6 +21011,7 @@ Cell type accession + Cell type ID beta12orEarlier Accession of a type or group of cells (catalogued in a database). @@ -21925,11 +21919,11 @@ - Protein torsion angle data - + Protein geometry report + Torsion angle data - Torsion angle data for a protein structure. beta12orEarlier + Geometry data for a protein structure, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc. @@ -23561,7 +23555,7 @@ Image metadata - + Image-associated data This can include basic provenance and technical information about the image, scientific annotation and so on. Any data concerning a specific biological or biomedical image. @@ -23616,6 +23610,89 @@ + + + + Disease identifier + + + + + + + + + beta12orEarlier + Identifier of an entry from a database of disease. + + + + + + + + + + + Disease name + + + The name of some disease. + 1.12 + + + + + + + + + + + Training material + + Open educational resource + Some material that is used for educational (training) purposes. + OER + 1.12 + + + + + + + + + + Online course + + MOOC + A training course available for use on the Web. + On-line course + 1.12 + Massive open online course + + + + + + + + + + Text + + + Any free or plain text, as often specified as some search query. + Plain text + Free text + 1.12 + + + + + + @@ -23666,12 +23743,12 @@ - inchikey + InChIKey + An InChIKey identifier is not human- nor machine-readable but is more suitable for web searches than an InChI chemical structure specification. The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound. beta12orEarlier - An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. @@ -26247,14 +26324,14 @@ - 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 + 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 + File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. @@ -26934,7 +27011,6 @@ plain text format (unformatted) - beta12orEarlier Plain text sequence format (essentially unformatted). @@ -29092,19 +29168,19 @@ - + - + - + BioXSD XML format @@ -29590,13 +29666,13 @@ - + - + Format of a bibliographic reference. @@ -30438,8 +30514,8 @@ + Format for mass pectra and derived data, include peptide sequences etc. 1.2 - Format for mass spectrometry data. @@ -31658,10 +31734,10 @@ xpm - 1.11 - Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type. X PixMap (XPM) is an image file format used by the X Window System, it is intended primarily for creating icon pixmaps, and supports transparent pixels. + 1.11 + Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type. @@ -31675,9 +31751,9 @@ rgb - 1.11 RGB file format is the native raster graphics file format for Silicon Graphics workstations. + 1.11 @@ -31691,9 +31767,9 @@ pbm - 1.11 The PBM format is a lowest common denominator monochrome file format. It serves as the common language of a large family of bitmap image conversion filters. + 1.11 @@ -31739,7 +31815,7 @@ svg - + The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999. Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation. @@ -32058,15 +32134,155 @@ + + + + MAT + + + + + + + + MATLAB file format + Binary format used by MATLAB files to store workspace variables. + 1.12 + MAT file format + .mat file format + + + + + + + + + + + netCDF + + 1.12 + ANDI-MS + Format used by netCDF software library for writing and reading chromatography-MS data files. + + + + + + + + + + + MGF + + Files includes *m*/*z*, intensity pairs separated by headers; headers can contain a bit more information, including search engine instructions. + Mascot Generic Format. Encodes multiple MS/MS spectra in a single file. + 1.12 + + + + + + + + + + dta + + Each file contains one header line for the known or assumed charge and the mass of the precursor peptide ion, calculated from the measured *m*/*z* and the charge. This one line was then followed by all the *m*/*z*, intensity pairs that represent the spectrum. + 1.12 + Spectral data format file where each spectrum is written to a separate file. + + + + + + + + + + pkl + + Spectral data file similar to dta. + Differ from .dta only in subtleties of the header line format and content and support the added feature of being able to. + 1.12 + + + + + + + + + + mzXML + + 1.12 + https://dx.doi.org/10.1038%2Fnbt1031 + Common file format for proteomics mass spectrometric data developed at the Seattle Proteome Center/Institute for Systems Biology. + + + + + + + + + + pepXML + + http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v118.xsd + Open data format for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans, intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses. + 1.12 + + + + + + + + + + GPML + + + Graphical Pathway Markup Language (GPML) is an XML format used + for exchanging biological pathways. + + + + + + + + + + + K-mer countgraph + + + 1.12 + File extension for this format is .oxlicg + http://www.iana.org/assignments/media-types/application/vnd.oxli.countgraph + A list of k-mers and their occurences in a dataset. Can also be used as an implicit De Bruijn graph. + + + + + + + Operation + A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). http://www.onto-med.de/ontologies/gfo.owl#Perpetuant Computational tool - A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state. Function http://purl.org/biotop/biotop.owl#Function http://www.ifomis.org/bfo/1.1/snap#Function @@ -32081,6 +32297,7 @@ Computational operation Computational subroutine http://semanticscience.org/resource/SIO_000649 + Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state. http://www.ifomis.org/bfo/1.1/span#Process http://www.ifomis.org/bfo/1.1/snap#Continuant http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method @@ -32100,20 +32317,20 @@ - Process - Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. + Computational tool + Computational tool provides one or more operations. - Computational tool provides one or more operations. - Computational tool + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. + Process - Function Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + Function @@ -32168,17 +32385,17 @@ Annotation - + - - + + - - + + Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. @@ -32194,7 +32411,7 @@ Indexing - + @@ -32330,14 +32547,14 @@ - - + + - - + + Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes. @@ -32356,14 +32573,14 @@ - - + + - - + + beta12orEarlier @@ -32401,14 +32618,14 @@ - - + + - - + + Motifs and patterns might be conserved or over-represented (occur with improbable frequency). @@ -32424,26 +32641,27 @@ - Sequence signature recognition + Sequence motif recognition - - + + - - + + beta12orEarlier + Sequence signature recognition + Motif scanning Motif search Sequence motif search Protein secondary database search Motif detection - Sequence motif recognition Sequence signature detection Sequence profile search Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s). @@ -32519,14 +32737,14 @@ - - + + - - + + This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. @@ -32614,12 +32832,7 @@ Residue interaction calculation - - - - - - + @@ -32645,7 +32858,7 @@ - Torsion angle calculation + Protein geometry calculation @@ -32653,8 +32866,16 @@ + WHATIF:ResidueTorsions beta12orEarlier + Backbone torsion angle calculation + WHATIF:CysteineTorsions Calculate, visualise or analyse phi/psi angles of a protein structure. + WHATIF:ResidueTorsionsBB + WHATIF:ShowTauAngle + Torsion angle calculation + Tau angle calculation + Cysteine torsion angle calculation @@ -32668,20 +32889,8 @@ - - - - - - - - - - - - - Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. This includes methods to render and visualise the properties of a protein sequence. + Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. beta12orEarlier Protein property rendering @@ -32708,9 +32917,13 @@ + Immunogenicity prediction beta12orEarlier This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. + This includes methods that generate a graphical rendering of antigenicity of a protein, such as a Hopp and Woods plot. + Hopp and Woods plotting Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins. + MHC peptide immunogenicity prediction @@ -32725,14 +32938,14 @@ - - + + - - + + Sequence feature prediction @@ -32786,19 +32999,19 @@ - + - - + + - - + + beta12orEarlier @@ -32971,12 +33184,6 @@ - - - - - - Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. Predict secondary structure of protein sequences. Secondary structure prediction (protein) @@ -33049,14 +33256,14 @@ - - + + - - + + Predict tertiary structure of a molecular (biopolymer) sequence. @@ -33117,12 +33324,13 @@ Protein-protein interaction prediction (from protein sequence) - - + beta12orEarlier + 1.12 + true Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences. - - + + @@ -33131,13 +33339,13 @@ Protein-protein interaction prediction (from protein structure) - - - + + true + 1.12 beta12orEarlier Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures. - - + + @@ -33191,12 +33399,6 @@ - - - - - - @@ -33213,18 +33415,12 @@ - Nucleic acid folding prediction + Nucleic acid folding analysis - - - - - - @@ -33232,6 +33428,7 @@ beta12orEarlier Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data. Nucleic acid folding modelling + Nucleic acid folding prediction Nucleic acid folding @@ -33367,31 +33564,31 @@ - + - - + + - + - - + + - - + + beta12orEarlier @@ -33412,14 +33609,14 @@ - - + + - - + + Identify and plot third base position variability in a nucleotide sequence. @@ -33451,14 +33648,14 @@ - - + + - - + + Sequence distance matrix construction @@ -33499,12 +33696,6 @@ - - - - - - @@ -33566,7 +33757,6 @@ Structure-based sequence alignment - Structure-based sequence alignment Sequence alignment generation (structure-based) Structure-based sequence alignment construction beta12orEarlier @@ -33612,20 +33802,20 @@ - - + + - - + + - - + + Sequence profile construction @@ -33645,20 +33835,20 @@ - - + + - - + + - + Structural profile generation @@ -33678,20 +33868,20 @@ - - + + - - + + - - + + Sequence profile alignment @@ -33711,17 +33901,16 @@ 3D profile-to-3D profile alignment - - - + + - - + + beta12orEarlier @@ -33782,14 +33971,14 @@ - - + + - - + + beta12orEarlier @@ -33812,14 +34001,14 @@ - - + + - - + + beta12orEarlier @@ -33840,12 +34029,6 @@ - - - - - - beta12orEarlier Protein domain prediction Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. @@ -33886,14 +34069,14 @@ - - + + - - + + beta12orEarlier @@ -34002,14 +34185,14 @@ - - + + - - + + @@ -34035,14 +34218,14 @@ - - + + - - + + beta12orEarlier @@ -34215,13 +34398,13 @@ - + - + beta12orEarlier @@ -34240,14 +34423,14 @@ - - + + - - + + beta12orEarlier @@ -34266,24 +34449,21 @@ - - - - - - - + - - + + + WHATIF: UseResidueDB Evaluate the quality or correctness a protein three-dimensional model. + This includes methods that calculate poor quality residues. The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. + Residue validation WHATIF: CorrectedPDBasXML Protein structure validation WHATIF: UseFileDB @@ -34315,7 +34495,7 @@ Phylogenetic tree generation - + @@ -34343,17 +34523,11 @@ Phylogenetic tree analysis - - - - - - - + - - + + beta12orEarlier @@ -34368,8 +34542,8 @@ Phylogenetic tree comparison + - beta12orEarlier Compare two or more phylogenetic trees. For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. @@ -34383,17 +34557,17 @@ Phylogenetic tree editing - + - + - + @@ -34456,18 +34630,13 @@ Protein SNP mapping - - - - - - - - + + true beta12orEarlier Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). - - + 1.12 + + @@ -34490,10 +34659,12 @@ - Methods might predict silent or pathological mutations. + Protein SNP mapping Protein mutation modelling Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function. + Rotamer likelihood prediction beta12orEarlier + This includes 1) rotamer likelihood prediction: the prediction of rotamer likelihoods for all 20 amino acid types at each position in a protein structure, where output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. 2) Protein SNP mapping, which maps and modesl the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). Methods might predict silent or pathological mutations. @@ -34522,14 +34693,14 @@ - - + + - - + + Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). @@ -34587,7 +34758,6 @@ Format validation - Test and validate the format and content of a data file. File format validation @@ -34605,22 +34775,23 @@ - - + + - + - - + + + Visualization beta12orEarlier Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. Rendering @@ -34638,12 +34809,6 @@ - - - - - - @@ -35042,6 +35207,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome annotation beta12orEarlier + Metagenome annotation Annotate a genome sequence with terms from a controlled vocabulary. @@ -35274,13 +35440,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydropathy calculation (from structure) - - - + + true Analyse the hydrophobic, hydrophilic or charge properties of a protein structure. + 1.12 beta12orEarlier - - + + @@ -35288,14 +35454,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Protein solvent accessibility calculation - - - - - - - + Accessible surface calculation + @@ -35303,7 +35463,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Calculate solvent accessible or buried surface areas in protein structures. + WHATIF:AtomAccessibilitySolventPlus + Protein solvent accessibility calculation + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + Calculate solvent accessible or buried surface areas in protein or other molecular structures. + WHATIF:AtomAccessibilitySolvent @@ -35314,12 +35478,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydropathy cluster calculation - - + + true + 1.12 beta12orEarlier Identify clusters of hydrophobic or charged residues in a protein structure. - - + + @@ -35346,16 +35511,22 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Protein surface and interior calculation - - - - - - - + Molecular surface calculation + + WHATIF:ResidueAccessibilityMolecular + Protein surface calculation + Protein surface and interior calculation + WHATIF:AtomAccessibilityMolecularPlus + WHATIF:TotAccessibilityMolecular + Protein atom surface calculation + Calculate the molecular surface area in proteins and other macromolecules. + Protein residue surface calculation + WHATIF:ResidueAccessibilityVacuum beta12orEarlier - Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc. + WHATIF:TotAccessibilitySolvent + WHATIF:ResidueAccessibilitySolvent + WHATIF:ResidueAccessibilityVacuumMolecular + WHATIF:AtomAccessibilityMolecular @@ -35366,14 +35537,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein binding site prediction (from structure) - - + Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures. beta12orEarlier - Ligand-binding and active site prediction (from structure) - Binding site prediction (from structure) - - + 1.12 + true + + @@ -35414,7 +35584,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein distance matrix calculation - + @@ -35433,7 +35603,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein contact map calculation - + @@ -35451,16 +35621,16 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Protein residue cluster calculation - + Residue cluster calculation + - Cluster of contacting residues might be key structural residues. Calculate clusters of contacting residues in protein structures. + This includes for example clusters of hydrophobic or charged residues, or clusters of contacting residues which have a key structural or functional role. beta12orEarlier @@ -35495,12 +35665,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue non-canonical interaction detection - - + beta12orEarlier + 1.12 Calculate non-canonical atomic interactions in protein structures. - - + true + + @@ -35556,14 +35727,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Calculate the molecular weight of a protein sequence or fragments. @@ -35600,14 +35771,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Calculate pH-dependent properties from pKa calculations of a protein sequence. @@ -35622,12 +35793,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydropathy calculation (from sequence) - - + + 1.12 Hydropathy calculation on a protein sequence. beta12orEarlier - - + true + + @@ -35694,7 +35866,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydrophobic region calculation - + Calculate hydrophobic or hydrophilic / charged regions of a protein sequence. beta12orEarlier @@ -35707,7 +35879,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein aliphatic index calculation - + @@ -35726,7 +35898,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein hydrophobic moment plotting - + @@ -35747,7 +35919,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein globularity prediction - + @@ -35766,7 +35938,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein solubility prediction - + @@ -35785,7 +35957,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein crystallizability prediction - + @@ -35830,11 +36002,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern MHC peptide immunogenicity prediction - + + true + Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc. beta12orEarlier - - + 1.12 + + @@ -35952,15 +36127,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein binding site prediction (from sequence) - - - Binding site prediction (from sequence) + + 1.12 Predict catalytic residues, active sites or other ligand-binding sites in protein sequences. - Ligand-binding and active site prediction (from sequence) - Protein binding site detection + true beta12orEarlier - - + + @@ -35969,7 +36142,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein-nucleic acid binding prediction - + beta12orEarlier Predict RNA and DNA-binding binding sites in protein sequences. @@ -36046,11 +36219,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Whole gene prediction - + beta12orEarlier + 1.12 + true Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc. - - + + @@ -36059,12 +36234,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene component prediction - + + true Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. beta12orEarlier Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences. - - + 1.12 + + @@ -36106,12 +36283,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - - - - - beta12orEarlier Quadruplex structure prediction Detect quadruplex-forming motifs in nucleotide sequences. @@ -36200,7 +36371,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Integrated gene prediction - + Predict whole gene structure using a combination of multiple methods to achieve better predictions. beta12orEarlier @@ -36213,7 +36384,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Operon prediction - + Find operons (operators, promoters and genes) in bacteria genes. beta12orEarlier @@ -36226,7 +36397,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Coding region prediction - + Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences. ORF prediction ORF finding @@ -36241,7 +36412,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Selenocysteine insertion sequence (SECIS) prediction - + @@ -36261,7 +36432,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Regulatory element prediction - + @@ -36491,6 +36662,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Sequence alignment analysis (indel detection) + Indel discovery Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. Identify insertion, deletion and duplication events from a sequence alignment. @@ -36668,7 +36840,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern tRNA gene prediction - + @@ -36812,12 +36984,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - - - - - @@ -36839,12 +37005,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - - - - - @@ -36906,12 +37066,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - - - - - @@ -36981,14 +37135,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -37013,12 +37167,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - - - - - Nucleic acid folding family identification RNA inverse folding beta12orEarlier @@ -37040,6 +37188,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Single nucleotide polymorphism detection beta12orEarlier This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. + SNP discovery @@ -37178,7 +37327,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pairwise sequence alignment generation - Pairwise sequence alignment Methods might perform one-to-one, one-to-many or many-to-many comparisons. Align exactly two molecular sequences. Pairwise sequence alignment construction @@ -37197,7 +37345,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Multiple sequence alignment construction Align two or more molecular sequences. This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. - Multiple sequence alignment beta12orEarlier Multiple sequence alignment generation @@ -37259,6 +37406,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment generation (local) Sequence alignment (local) Locally align two or more molecular sequences. + Smith-Waterman @@ -37393,18 +37541,17 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + RNA secondary structure alignment generation - RNA secondary structure alignment Align RNA secondary structures. RNA secondary structure alignment construction Secondary structure alignment (RNA) @@ -37762,10 +37909,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Sequence assembly (mapping assembly) + Mapping assembly Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome. beta12orEarlier + Sequence assembly (mapping assembly) The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. @@ -37776,9 +37924,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Sequence assembly (de-novo assembly) + De-novo assembly + De Bruijn graph Sequence assembly by combining fragments without the aid of a reference sequence or genome. + Sequence assembly (de-novo assembly) De-novo assemblers are much slower and more memory intensive than mapping assemblers. beta12orEarlier @@ -37790,10 +37940,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Sequence assembly (genome assembly) + Genome assembly - Sequence assembly capable on a very large scale such as assembly of whole genomes. + The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. beta12orEarlier + Sequence assembly (genome assembly) @@ -37803,9 +37954,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Sequence assembly (EST assembly) + EST assembly beta12orEarlier + Sequence assembly (EST assembly) Sequence assembly for EST sequences (transcribed mRNA). Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. @@ -38077,14 +38229,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Phylogenetic tree construction (from gene frequencies) @@ -38211,19 +38363,19 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + + Identify a plausible model of DNA substitution that explains a molecular (DNA or protein) sequence alignment. Sequence alignment analysis (phylogenetic modelling) beta12orEarlier - Identify a plausible model of DNA substitution that explains a DNA sequence alignment. @@ -38363,30 +38515,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Immunogenicity prediction - - - - - - - - - - - - - - - - - - - + + true + 1.12 beta12orEarlier Peptide immunogen prediction Predict and optimise peptide ligands that elicit an immunological response. - - + + @@ -38395,17 +38531,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern DNA vaccine design - - - - - - - @@ -38421,24 +38550,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence formatting - - - - - - - - - - - - - + + 1.12 beta12orEarlier Reformat (a file or other report of) molecular sequence(s). - Sequence file format conversion - - + true + + @@ -38447,23 +38565,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment formatting - - - - - - - - - - - - - + Reformat (a file or other report of) molecular sequence alignment(s). beta12orEarlier - - + true + 1.12 + + @@ -38472,24 +38580,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Codon usage table formatting - - - - - - - - - - - - - - + Reformat a codon usage table. + true beta12orEarlier - - + 1.12 + + @@ -38559,12 +38656,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - - - - - Sequence cluster rendering beta12orEarlier Visualise, format or render sequence clusters. @@ -38578,8 +38669,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree visualisation + - @@ -38644,14 +38735,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Structure rendering @@ -38991,7 +39082,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Surface rendering - + beta12orEarlier WHATIF:GetSurfaceDots Calculate the positions of dots that are homogeneously distributed over the surface of a molecule. @@ -39006,14 +39097,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein atom surface calculation (accessible) - + beta12orEarlier - WHATIF:AtomAccessibilitySolventPlus - WHATIF:AtomAccessibilitySolvent + 1.12 + true Calculate the solvent accessibility ('accessible surface') for each atom in a structure. Waters are not considered. - - + + @@ -39022,14 +39113,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein atom surface calculation (accessible molecular) - + beta12orEarlier + 1.12 Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. Waters are not considered. - WHATIF:AtomAccessibilityMolecular - WHATIF:AtomAccessibilityMolecularPlus - - + true + + @@ -39038,13 +39129,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation (accessible) - - WHATIF:ResidueAccessibilitySolvent + + true + 1.12 beta12orEarlier Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). Calculate the solvent accessibility ('accessible surface') for each residue in a structure. - - + + @@ -39053,13 +39145,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation (vacuum accessible) - + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. - WHATIF:ResidueAccessibilityVacuum + 1.12 + true beta12orEarlier - - + + @@ -39068,13 +39161,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation (accessible molecular) - + Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. - WHATIF:ResidueAccessibilityMolecular + true Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + 1.12 beta12orEarlier - - + + @@ -39083,13 +39177,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation (vacuum molecular) - + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + true beta12orEarlier Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. - WHATIF:ResidueAccessibilityVacuumMolecular - - + 1.12 + + @@ -39098,12 +39193,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein surface calculation (accessible molecular) - - WHATIF:TotAccessibilityMolecular + + true + 1.12 beta12orEarlier Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. - - + + @@ -39112,12 +39208,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein surface calculation (accessible) - - WHATIF:TotAccessibilitySolvent + Calculate the solvent accessibility ('accessible surface') for a structure as a whole. beta12orEarlier - - + 1.12 + true + + @@ -39126,12 +39223,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Backbone torsion angle calculation - + + 1.12 beta12orEarlier - WHATIF:ResidueTorsionsBB + true Calculate for each residue in a protein structure all its backbone torsion angles. - - + + @@ -39140,12 +39238,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Full torsion angle calculation - + + 1.12 beta12orEarlier Calculate for each residue in a protein structure all its torsion angles. - WHATIF:ResidueTorsions - - + true + + @@ -39154,12 +39253,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Cysteine torsion angle calculation - + beta12orEarlier Calculate for each cysteine (bridge) all its torsion angles. - WHATIF:CysteineTorsions - - + 1.12 + true + + @@ -39168,13 +39268,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Tau angle calculation - - WHATIF:ShowTauAngle + beta12orEarlier Tau is the backbone angle N-Calpha-C (angle over the C-alpha). + 1.12 For each amino acid in a protein structure calculate the backbone angle tau. - - + true + + @@ -39212,6 +39313,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Metal-bound cysteine detection + beta12orEarlier WHATIF:ShowCysteineMetal @@ -39226,15 +39328,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation (residue-nucleic acid) - - - + beta12orEarlier - WHATIF:ShowProteiNucleicContacts + 1.12 + true Calculate protein residue contacts with nucleic acids in a structure. - WHATIF:HasNucleicContacts - - + + @@ -39242,13 +39342,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Residue contact calculation (residue-metal) - - - WHATIF:HasMetalContacts + Protein-metal contact calculation + beta12orEarlier Calculate protein residue contacts with metal in a structure. - WHATIF:HasMetalContactsPlus + Residue-metal contact calculation @@ -39259,13 +39357,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation (residue-negative ion) - + Calculate ion contacts in a structure (all ions for all side chain atoms). - WHATIF:HasNegativeIonContactsPlus beta12orEarlier - WHATIF:HasNegativeIonContacts - - + true + 1.12 + + @@ -39274,7 +39372,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue bump detection - + WHATIF:ShowBumps beta12orEarlier Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance. @@ -39288,13 +39386,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue symmetry contact calculation - + Calculate the number of symmetry contacts made by residues in a protein structure. + true + 1.12 WHATIF:SymmetryContact A symmetry contact is a contact between two atoms in different asymmetric unit. beta12orEarlier - - + + @@ -39303,15 +39403,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation (residue-ligand) - - + + true beta12orEarlier + 1.12 Calculate contacts between residues and ligands in a protein structure. - WHATIF:ShowDrugContactsShort - WHATIF:ShowLigandContacts - WHATIF:ShowDrugContacts - - + + @@ -39320,7 +39418,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Salt bridge calculation - + Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. WHATIF:HasSaltBridgePlus WHATIF:ShowSaltBridges @@ -39338,13 +39436,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Rotamer likelihood prediction - + WHATIF:ShowLikelyRotamers WHATIF:ShowLikelyRotamers500 + 1.12 Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure. - WHATIF:ShowLikelyRotamers800 WHATIF:ShowLikelyRotamers600 + WHATIF:ShowLikelyRotamers800 WHATIF:ShowLikelyRotamers900 + true Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. WHATIF:ShowLikelyRotamers700 WHATIF:ShowLikelyRotamers400 @@ -39352,8 +39452,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern WHATIF:ShowLikelyRotamers200 WHATIF:ShowLikelyRotamers100 beta12orEarlier - - + + @@ -39362,12 +39462,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Proline mutation value calculation - + + true + 1.12 Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein. WHATIF:ProlineMutationValue beta12orEarlier - - + + @@ -39376,7 +39478,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue packing validation - + beta12orEarlier Identify poorly packed residues in protein structures. WHATIF: PackingQuality @@ -39389,11 +39491,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Dihedral angle validation + Protein geometry validation WHATIF: ImproperQualitySum - Identify for each residue in a protein structure any improper dihedral (phi/psi) angles. beta12orEarlier + Validate protein geometry, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc. WHATIF: ImproperQualityMax @@ -39421,13 +39523,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern HET group detection - + + true Identify HET groups in PDB files. - WHATIF: HETGroupNames beta12orEarlier + 1.12 A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. - - + + @@ -39452,12 +39555,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure formatting - + + 1.12 + true Reformat (a file or other report of) tertiary structure data. beta12orEarlier WHATIF: PDBasXML - - + + @@ -39485,13 +39590,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue validation - + + 1.12 Identify poor quality amino acid positions in protein structures. beta12orEarlier - WHATIF: UseResidueDB - The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). - - + true + + @@ -39641,12 +39746,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Representative sequence identification - - - - - - Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences. beta12orEarlier @@ -39691,10 +39790,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Statistical calculation + Statistics + Statistical testing Statistical analysis Perform a statistical data operation of some type, e.g. calibration or validation. + Gibbs sampling beta12orEarlier - true @@ -39813,7 +39914,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence analysis - + @@ -39867,14 +39968,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Structure analysis (protein) @@ -39919,8 +40020,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Utility operation - + File handling + @@ -39931,8 +40032,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern File processing beta12orEarlier Report handling - File handling Data file processing + Utility operation @@ -40029,14 +40130,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + This is a broad concept and is used a placeholder for other, more specific concepts. @@ -40115,14 +40216,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Operation (typed) - - Computation - Calculation - Processing + + true Process (read and / or write) data of a specific type, for example applying analytical methods. beta12orEarlier - - + 1.12 + + @@ -40171,7 +40271,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Prediction and recognition - + beta12orEarlier Recognition Prediction @@ -40187,7 +40287,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Comparison - + beta12orEarlier Compare two or more things to identify similarities. @@ -40200,7 +40300,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Optimisation and refinement - + beta12orEarlier Refine or optimise some data model. @@ -40213,7 +40313,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Modelling and simulation - + @@ -40221,7 +40321,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Model or simulate some biological entity or system. + Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. + Mathematical modelling @@ -40247,9 +40348,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Validation - + beta12orEarlier Validation and standardisation + Quality control Validate some data. @@ -40261,7 +40363,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Mapping - + This is a broad concept and is used a placeholder for other, more specific concepts. Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts. beta12orEarlier @@ -40275,7 +40377,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Design - + beta12orEarlier Design a biological entity (typically a molecular sequence or structure) with specific properties. true @@ -40355,10 +40457,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern + Analyse a set of genes (genes corresponding to an expression profile, or any other set) to find functional annotations (such as cellular processes or metaobolic pathways) that the sets are significantly associated with, providing biological insight into the a set of genes. beta12orEarlier - Gene expression profile annotation The Gene Ontology (GO) is invariably used, the input is a set of Gene IDs and the output of the analysis is typically a ranked list of GO terms, each associated with a p-value. - Analyse a set of genes (genes corresponding to an expression profile, or any other set) with respect to concepts from an ontology of gene functions. GO term enrichment @@ -40396,17 +40497,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pathway or network processing - - - - - - - + Generate, analyse or handle a biological pathway or network. beta12orEarlier - - + true + 1.12 + + @@ -40487,17 +40584,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Phylogenetic tree processing - - - - - - - + beta12orEarlier - Process (read and / or write) a phylogenetic tree. - - + 1.12 + true + Generate, process or analyse phylogenetic tree or trees. + + @@ -40592,12 +40685,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - - - - - @@ -40647,19 +40734,22 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + + Gene component prediction + Detect, predict and identify genes or components of genes in DNA sequences, including promoters, coding regions, splice sites, etc. + Whole gene prediction Gene and gene component prediction beta12orEarlier - Detect, predict and identify genes or components of genes in DNA sequences. + Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. Gene finding @@ -40728,12 +40818,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein atom surface calculation - + Waters are not considered. Calculate the solvent accessibility for each atom in a structure. beta12orEarlier - - + 1.12 + true + + @@ -40742,11 +40834,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue surface calculation - + beta12orEarlier + true Calculate the solvent accessibility for each residue in a structure. - - + 1.12 + + @@ -40755,11 +40849,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein surface calculation - + beta12orEarlier Calculate the solvent accessibility of a structure as a whole. - - + 1.12 + true + + @@ -40783,6 +40879,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein-protein interaction prediction + @@ -40983,20 +41080,20 @@ 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. @@ -41059,7 +41156,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure analysis - + @@ -41082,14 +41179,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse nucleic acid tertiary structural data. @@ -41241,11 +41338,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Residue contact calculation (residue-residue) - + + true beta12orEarlier Calculate contacts between residues in a protein structure. - - + 1.12 + + @@ -41254,12 +41353,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Hydrogen bond calculation (inter-residue) - - + Identify potential hydrogen bonds between amino acid residues. + 1.12 + true beta12orEarlier - - + + @@ -41309,18 +41409,19 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene expression data analysis - + - beta12orEarlier - Gene expression profile analysis Gene expression (microarray) data processing + Gene expression profile analysis + beta12orEarlier Microarray data processing Gene expression data processing + Gene expression analysis Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms. @@ -41346,15 +41447,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pathway or network analysis - + - - + + - Analyse a known biological pathway or network. Pathway analysis + Generate, process or analyse a biological pathway or network. Network analysis beta12orEarlier @@ -41419,7 +41520,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Nucleic acid analysis - + @@ -41439,11 +41540,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein analysis - + - + beta12orEarlier @@ -41727,14 +41828,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -41791,15 +41892,18 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein binding site prediction + - Ligand-binding and active site prediction beta12orEarlier + Active site prediction Binding site prediction + Protein binding site detection + Ligand-binding site prediction Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures. @@ -41832,7 +41936,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Alignment - + @@ -41841,7 +41945,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits. - Alignment Alignment generation beta12orEarlier Alignment construction @@ -41907,12 +42010,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Hopp and Woods plotting - - + beta12orEarlier + 1.12 Generate a Hopp and Woods plot of antigenicity of a protein. - - + true + + @@ -42090,10 +42194,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Analysis - Apply analytical methods to existing data of a specific type. - For non-analytical operations, see the 'Processing' branch. + Process or apply analytical methods to existing data of a specific type. + Processing beta12orEarlier - @@ -42122,12 +42225,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - - - - - @@ -42138,9 +42235,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern + + + + + + Analyse a body of scientific text (typically a full text article from a scientific journal.) beta12orEarlier - Article analysis @@ -42189,10 +42291,27 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Residue contact calculation + Residue distance calculation - Calculate contacts between residues and some other group in a protein structure. + WHATIF:HasNegativeIonContacts + Residue contact calculation (residue-ligand) + Residue contact calculation (residue-metal) + WHATIF:SymmetryContact + Residue contact calculation (residue-negative ion) + This includes identifying HET groups, which usually correspond to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. It can also include calculation of symmetry contacts, i.e. a contact between two atoms in different asymmetric unit. + WHATIF:HasMetalContactsPlus + Calculate contacts between residues, or between residues and other groups, in a protein structure, on the basis of distance calculations. + Residue contact calculation (residue-nucleic acid) + WHATIF: HETGroupNames + HET group detection + WHATIF:ShowDrugContacts + WHATIF:ShowLigandContacts + WHATIF:HasNucleicContacts + WHATIF:ShowDrugContactsShort + WHATIF:ShowProteiNucleicContacts beta12orEarlier + WHATIF:HasMetalContacts + WHATIF:HasNegativeIonContactsPlus @@ -42292,7 +42411,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Classification - + beta12orEarlier Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category. @@ -42432,7 +42551,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pathway or network visualisation - + @@ -42522,14 +42641,14 @@ 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. @@ -42567,14 +42686,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta13 @@ -42603,7 +42722,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Editing - + beta13 Edit a data entity, either randomly or specifically. @@ -42620,8 +42739,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + @@ -42632,12 +42751,16 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - 1.1 + Assembly quality evaluation + Assembly QC + Sequence assembly quality evaluation + Sequence assembly QC Evaluate a DNA sequence assembly, typically for purposes of quality control. + 1.1 @@ -42652,7 +42775,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Align two or more (tpyically huge) molecular sequences that represent genomes. Genome alignment construction 1.1 - Genome alignment @@ -42749,12 +42871,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Trim ends - + 1.1 Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. + 1.12 For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. - - + true + + @@ -42763,11 +42887,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Trim vector - + + true Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. + 1.12 1.1 - - + + @@ -42776,11 +42902,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Trim to reference - + + true 1.1 + 1.12 Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. - - + + @@ -42791,7 +42919,23 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence trimming 1.1 + Trim to reference Cut (remove) the end from a molecular sequence. + Trim vector + Trimming + Trim ends + This includes + +ennd trimming +Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. +For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. + +trimming to a reference sequence, +Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. + +vector trimming +Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. + @@ -43022,7 +43166,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome visualization Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence. Genome rendering - Genome visualisation + Genome browser Genome viewing Genome browsing @@ -43056,8 +43200,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. + Genome indexing (Burrows-Wheeler) + Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. A suffix array consists of the lexicographically sorted list of suffixes of a genome. + Genome indexing (suffix arrays) Generate an index of a genome sequence. + Suffix arrays + Burrows-Wheeler 1.1 @@ -43069,12 +43217,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome indexing (Burrows-Wheeler) - + The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. + 1.12 + true Generate an index of a genome sequence using the Burrows-Wheeler algorithm. 1.1 - - + + @@ -43083,13 +43233,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome indexing (suffix arrays) - + 1.1 Generate an index of a genome sequence using a suffix arrays algorithm. - suffix arrays A suffix array consists of the lexicographically sorted list of suffixes of a genome. - - + true + 1.12 + Suffix arrays + + @@ -43099,10 +43251,16 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Spectral analysis - Spectral analysis + + + + + + + Spectrum analysis 1.1 + Analyse one or more spectra from mass spectrometry (or other) experiments. Spectrum analysis - Analyse a spectrum from a mass spectrometry (or other) experiment. Mass spectrum analysis @@ -43188,11 +43346,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Read pre-processing - + Sequence read pre-processing - This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. Pre-process sequence reads to ensure (or improve) quality and reliability. + For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. 1.1 @@ -43224,7 +43382,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Peak calling - Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). + Peak-pair calling + Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). "Peak-pair calling" is similar to "Peak calling" in the context of ChIP-exo. Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. Protein binding peak detection 1.1 @@ -43297,10 +43456,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Variant calling + Allele calling + Somatic variant calling + Germ line variant calling + Somatic variant calling is the detection of variations established in somatic cells and hence not inherited as a germ line variant. + Methods often utilise a database of aligned reads. Variant mapping 1.1 + Variant detection Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence. - Methods often utilise a database of aligned reads. @@ -43324,11 +43488,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern + Exome assembly Exome analysis - + 1.1 - Targeted exome capture - Exome sequencing is considered a cheap alternative to whole genome sequencing. Exome sequence analysis Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome. @@ -43394,6 +43557,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.2 Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). + Adapter removal @@ -43546,7 +43710,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Anonymisation - + Process data in such a way that makes it hard to trace to the person which the data concerns. 1.3 Data anonymisation @@ -43642,10 +43806,22 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Protein surface analysis - + Molecular surface analysis + + + + + + + + + + + + + 1.4 - Analyse the surface properties of proteins. + Analyse the surface properties of proteins or other macromolecules, including surface accessible pockets, interior inaccessible cavities etc. @@ -43686,14 +43862,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Recognition of which format the given data is in. @@ -43708,8 +43884,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 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. - + @@ -43733,7 +43909,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Generation - + Construction beta12orEarlier For non-analytical operations, see the 'Processing' branch. @@ -43784,7 +43960,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Clustering - + 1.6 Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters). @@ -43797,7 +43973,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Assembly - + 1.6 Construct some entity (typically a molecule sequence) from component pieces. @@ -43810,9 +43986,9 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Conversion - + + Convert a data set from one form to another. 1.6 - Non-analytical data conversion. @@ -43823,8 +43999,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Standardization and normalization - + + Normalization 1.6 + Standardization Standardize or normalize data. @@ -43862,7 +44040,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Calculation - + Mathemetical determination of the value of something, typically a properly of a molecule. 1.6 @@ -43876,7 +44054,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Pathway or network prediction - + 1.6 Predict a molecular pathway or network. @@ -43889,11 +44067,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Genome assembly - + + 1.12 1.6 The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. + true + - + @@ -43902,7 +44083,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Plotting - + Generate a graph, or other visual representation, of data, showing the relationship between two or more variables. 1.6 @@ -43915,7 +44096,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Image analysis - + @@ -44162,7 +44343,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Correlation - + @@ -44214,7 +44395,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Nucleic acid alignment folding prediction (alignment-based) + Nucleic acid folding prediction (alignment-based) 1.7 Prediction of nucleic-acid folding using sequence alignments as a source of data. @@ -44309,8 +44490,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Enrichment + - @@ -44378,11 +44559,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Mathematical modelling - + + 1.12 Model some biological system using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. + true beta12orEarlier - - + + @@ -44427,7 +44610,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Data imputation Replace missing data with substituted values, usually by using some statistical or other mathematical approach. - true 1.9 @@ -44551,6 +44733,546 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern + + + + Relationship inference + + + + + + + + + + + + + + + + + + + + 1.12 + Identify semantic relationships within a text or between two or more texts using text mining techniques. + + + + + + + + + + Mass spectra calibration + + + + + + + + Re-adjust the output of mass spectrometry experiments with shifted ppm values. + 1.12 + + + + + + + + + + Chromatographic alignment + + + + + + + + Align multiple data sets using information from chromatography and/or peptide identification, from mass spectrometry experiments. + 1.12 + + + + + + + + + + Deisotoping + + + + + + + + The removal of isotope peaks in a spectrum, to represent the fragment ion as one data point. + Deconvolution + 1.12 + Deisotoping is commonly done to reduce complexity, and done in conjunction with the charge state deconvolution. + + + + + + + + + + Quantification + + + + + + + + Technique for determining the amount of proteins in a sample. + 1.12 + Quantitation + + + + + + + + + + Peptide identification + + + + + + + + Peptide-spectrum-matching + Determination of peptide sequence from mass spectrum. + 1.12 + + + + + + + + + + Isotopic distributions calculation + + + + + + + + + + + + + + Peptide-spectrum-matching + Predict the isotope distribution of a given chemical species. + 1.12 + + + + + + + + + + Retention times calculation + + Prediction of retention times in a mass spectrometry experiment based on compositional and structural properties of the separated species. + 1.12 + + + + + + + + + + Label-free quantification + + 1.12 + Quantification without the use of chemical tags. + + + + + + + + + + Labeled quantification + + 1.12 + Quantification based on the use of chemical tags. + + + + + + + + + + MRM/SRM + + 1.12 + Quantification by Selected/multiple Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair). + + + + + + + + + + Spectral counting + + 1.12 + Calculate number of identified MS2 spectra as approximation of peptide / protein quantity. + + + + + + + + + + SILAC + + Quantification analysis using stable isotope labeling by amino acids in cell culture. + 1.12 + + + + + + + + + + iTRAQ + + 1.12 + Quantification analysis using the AB SCIEX iTRAQ isobaric labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near 114 m/z. + + + + + + + + + + 18O labeling + + 1.12 + Quantification analysis using labeling based on 18O-enriched H2O. + + + + + + + + + + TMT-tag + + 1.12 + Quantification analysis using the Thermo Fisher tandem mass tag labelling workflow. + + + + + + + + + + Dimethyl + + 1.12 + Quantification analysis using chemical labeling by stable isotope dimethylation + + + + + + + + + + Tag-based peptide identification + + Peptide sequence tags are used as piece of information about a peptide obtained by tandem mass spectrometry. + 1.12 + + + + + + + + + + de Novo sequencing + + + Analytical process that derives a peptide’s amino acid sequence from its tandem mass spectrum (MS/MS) without the assistance of a sequence database. + 1.12 + + + + + + + + + + PTM identification + + Identification of post-translational modifications (PTMs) of peptides/proteins in mass spectrum. + 1.12 + + + + + + + + + + Peptide database search + + + 1.12 + Determination of best matches between MS/MS spectrum and a database of protein or nucleic acid sequences. + + + + + + + + + + Blind peptide database search + + Modification-tolerant peptide database search + Unrestricted peptide database search + 1.12 + Peptide database search for identification of known and unknown PTMs looking for mass difference mismatches. + + + + + + + + + + Validation of peptide-spectrum matches + + + Statistical estimation of false discovery rate from score distribution for peptide-spectrum-matches, following a peptide database search. + 1.12 + + + + + + + + + + Target-Decoy + + Estimation of false discovery rate by comparison to search results with a database containing incorrect information. + 1.12 + + + + + + + + + + Statistical inference + + 1.12 + Empirical Bayes + Analyse data in order to deduce properties of an underlying distribution or population. + + + + + + + + + + Regression analysis + + A statistical calculation to estimate the relationships among variables. + Regression + 1.12 + + + + + + + + + + Metabolic network modelling + + + + + + + + Model a metabolic network, for example, to reconstruct pathways or to simulate metabolism. + Metabolic reconstruction + Metabolic network reconstruction + Metabolic network simulation + 1.12 + + + + + + + + + + SNP annotation + + Predict the effect or function of an individual single nucleotide polymorphism (SNP). + 1.12 + + + + + + + + + + Ab-initio gene prediction + + Prediction of genes or gene components from first principles, i.e. without reference to existing genes. + 1.12 + Gene prediction (ab-initio) + + + + + + + + + + Homology-based gene prediction + + Gene prediction (homology-based) + Prediction of genes or gene components by reference to homologous genes. + 1.12 + + + + + + + + + + Statistical modelling + + 1.12 + Construction of a statistical model, or a set of assumptions around some observed data, usually by describing a set of probability distributions which approximate the distribution of data. + + + + + + + + + + Molecular surface comparison + + + 1.12 + Compare two or more molecular surfaces. + + + + + + + + + + Gene functional annotation + + 1.12 + Annotate one or more sequences with functional information, such as cellular processes or metaobolic pathways, by reference to a controlled vocabulary - invariably the Gene Ontology (GO). + + + + + + + + + + Variant filtering + + + 1.12 + Variant filtering is used to eliminate false positive variants based for example on base calling quality, strand and position information, and mapping info. + + + + + + + + + + Differential binding analysis + + 1.12 + Differential binding analysis identifies binding sites in nucleic acid sequences that are statistically significantly differentially bound between sample groups. + + + + + + @@ -44651,7 +45373,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Computational structural biology 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 Structure databases This includes related concepts such as structural properties, alignments and structural motifs. @@ -44669,8 +45390,18 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Structure prediction + Protein fold recognition + The prediction of molecular structure, including the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features, and the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. + + + Nucleic acid structure prediction beta12orEarlier - The prediction of molecular (secondary or tertiary) structure. + Protein structure prediction + DNA structure prediction + Nucleic acid design + Nucleic acid folding + RNA structure prediction + This includes the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s), for example by threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). @@ -44840,6 +45571,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern RNA beta12orEarlier + Small RNA RNA sequences and structures. @@ -44867,15 +45599,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Mapping + 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. It also covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. + DNA mapping + beta12orEarlier + The mapping of complete (typically nucleotide) sequences. Mapping (in the sense of short read alignment, or more generally, just alignment) has application in RNA-Seq analysis (mapping of transcriptomics reads), variant discovery (e.g. mapping of exome capture), and re-sequencing (mapping of WGS reads). 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. - @@ -44983,6 +45714,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern This includes the study of promoters, coding regions etc. beta12orEarlier + Fusion genes Gene features Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. @@ -45192,7 +45924,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein residue interactions The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. - Protein residue interactions true 1.3 beta12orEarlier @@ -45297,6 +46028,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Lipids beta12orEarlier + Lipidomics Lipids and their structures. @@ -45313,6 +46045,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. CHEBI:23367 beta12orEarlier + Chemical structures @@ -45373,12 +46106,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence comparison - + + true The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. beta12orEarlier + 1.12 The comparison of two or more molecular sequences, for example sequence alignment and clustering. - - + + @@ -45387,7 +46122,7 @@ 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. @@ -45476,12 +46211,13 @@ positional features such as functional and other key sites, in molecular sequenc Protein structure prediction - - + + true beta12orEarlier The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. - - + 1.12 + + @@ -45490,16 +46226,13 @@ 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 + 1.12 + true beta12orEarlier - Nucleic acid folding - - + + @@ -45555,11 +46288,13 @@ positional features such as functional and other key sites, in molecular sequenc Molecular docking - + beta12orEarlier + true The modelling the structure of proteins in complex with small molecules or other macromolecules. - - + 1.12 + + @@ -45600,12 +46335,13 @@ 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). + + 1.12 The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). + true beta12orEarlier - - + + @@ -45730,7 +46466,7 @@ positional features such as functional and other key sites, in molecular sequenc Assembly 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. + Assembly has two broad types, de-novo and re-sequencing. Re-sequencing is a specialized case of assembly, where an assembled (typically de-novo assembled) reference genome is available and is about 95% identical to the re-sequenced genome. All other cases of assembly are 'de-novo'. @@ -45741,14 +46477,15 @@ positional features such as functional and other key sites, in molecular sequenc Genetic variation - + - 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 + Polymorphism + Somatic mutations + 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. + http://purl.bioontology.org/ontology/MSH/D014644 + DNA variation @@ -45795,6 +46532,7 @@ 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. + Transcription Gene expression profiling Expression profiling beta12orEarlier @@ -45817,6 +46555,7 @@ positional features such as functional and other key sites, in molecular sequenc Gene regulation + Regulatory genomics beta12orEarlier The regulation of gene expression. @@ -45832,6 +46571,7 @@ positional features such as functional and other key sites, in molecular sequenc beta12orEarlier + Pharmacogenetics The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. @@ -45935,14 +46675,13 @@ positional features such as functional and other key sites, in molecular sequenc - Data mining + Text mining beta12orEarlier - Text data mining The analysis of the biomedical and informatics literature. Literature analysis - Text mining Literature mining + Text data mining @@ -45953,10 +46692,10 @@ positional features such as functional and other key sites, in molecular sequenc - Data deposition, annotation and curation + Data submission, annotation and curation + Database curation Deposition and curation of database accessions, including annotation, typically with terms from a controlled vocabulary. - Database curation beta12orEarlier @@ -46043,12 +46782,14 @@ positional features such as functional and other key sites, in molecular sequenc Sequence classification - + + 1.12 + true beta12orEarlier 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. - - + + @@ -46107,6 +46848,8 @@ positional features such as functional and other key sites, in molecular sequenc Molecular interactions, pathways and networks + Networks + Pathways Biological networks Network or pathway analysis beta13 @@ -46114,6 +46857,7 @@ positional features such as functional and other key sites, in molecular sequenc Biological models Molecular interactions, biological pathways, networks and other models. Biological pathways + Interactions http://edamontology.org/topic_3076 @@ -46329,6 +47073,7 @@ positional features such as functional and other key sites, in molecular sequenc Drug structures beta12orEarlier The structures of drugs, drug target, their interactions and binding affinities. + Drug targets Target structures @@ -46359,6 +47104,7 @@ positional features such as functional and other key sites, in molecular sequenc Genomics http://purl.bioontology.org/ontology/MSH/D023281 + Personal genomics beta12orEarlier Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. @@ -46435,16 +47181,12 @@ positional features such as functional and other key sites, in molecular sequenc - Sequence design + Probes and primers Probes 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 - in silico cloning - Primer design Primers beta12orEarlier @@ -46458,6 +47200,7 @@ positional features such as functional and other key sites, in molecular sequenc Pathology + Disease Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. beta12orEarlier Diseases @@ -46582,6 +47325,7 @@ positional features such as functional and other key sites, in molecular sequenc DNA analysis beta12orEarlier + Ancient DNA DNA sequences and structure, including processes such as methylation and replication. The DNA sequences might be coding or non-coding sequences. @@ -46613,13 +47357,23 @@ positional features such as functional and other key sites, in molecular sequenc Functional, regulatory and non-coding RNA + small interfering RNA + small nucleolar RNA ncRNA Non-coding RNA Functional RNA + snRNA 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). + Regulatory RNA + siRNA + piRNA + snoRNA + small nuclear RNA beta12orEarlier + miRNA + microRNA + piwi-interacting RNA @@ -46816,7 +47570,7 @@ positional features such as functional sites in nucleotide sequences. Transcription factors and regulatory sites - + 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. 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. @@ -46892,12 +47646,11 @@ positional features such as functional sites in nucleotide sequences. Workflows - + + Pipelines Biological or biomedical analytical workflows or pipelines. beta12orEarlier - true - 1.0 - + @@ -47271,7 +48024,7 @@ 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) @@ -47533,13 +48286,14 @@ positional features such as functional sites in nucleotide sequences. Molecular modelling + Molecular docking Homology modeling - Comparative modeling - Comparative modelling beta12orEarlier + Comparative modelling Homology modelling Molecular modeling - The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. + Comparative modeling + The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour, including the modelling the structure of proteins in complex with small molecules or other macromolecules (docking). @@ -47989,7 +48743,6 @@ positional features such as functional sites in nucleotide sequences.Toxins and the adverse effects of these chemical substances on living organisms. VT 3.1.9 Toxicology Toxicoinformatics - Toxicology beta12orEarlier Computational toxicology @@ -48069,7 +48822,6 @@ positional features such as functional sites in nucleotide sequences.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. @@ -48084,9 +48836,7 @@ positional features such as functional sites in nucleotide sequences.Microsatellites beta12orEarlier - Nucleic acid features (microsatellite) 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. @@ -48102,9 +48852,7 @@ positional features such as functional sites in nucleotide sequences. 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 - Nucleic acid features (RFLP) @@ -48120,7 +48868,6 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid features (polymorphism) DNA polymorphism. - Polymorphism annotation beta12orEarlier @@ -48368,7 +49115,7 @@ positional features such as functional sites in nucleotide sequences.Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). true beta13 - + @@ -48475,10 +49222,10 @@ positional features such as functional sites in nucleotide sequences. Literature and reference - Literature search beta13 The scientific literature, reference information and documentation. Literature sources + Bibliography http://purl.bioontology.org/ontology/MSH/D011642 @@ -48559,7 +49306,7 @@ positional features such as functional sites in nucleotide sequences.true beta13 1.3 - + @@ -48659,14 +49406,13 @@ positional features such as functional sites in nucleotide sequences. Expression signals - - + beta13 - Nucleic acid features (expression signal) + true + 1.12 Regions within a nucleic acid sequence containing a signal that alters a biological function. - - - + + @@ -48757,12 +49503,17 @@ positional features such as functional sites in nucleotide sequences. Sequencing + Resequencing http://purl.bioontology.org/ontology/MSH/D059014 - 1.1 + Chromosome walking NGS + Next gen sequencing + DNA-Seq + High throughput sequencing + 1.1 + Primer walking 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 @@ -48774,16 +49525,14 @@ positional features such as functional sites in nucleotide sequences. ChIP-seq - - true - 1.3 + + 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 Seq Chip-sequencing - - + @@ -48792,19 +49541,17 @@ positional features such as functional sites in nucleotide sequences. RNA-Seq - + Small RNA-seq Whole transcriptome shotgun sequencing RNA-seq + miRNA-seq 1.1 - 1.3 A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. Small RNA-Seq WTSS This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. - true - - + @@ -48819,7 +49566,7 @@ positional features such as functional sites in nucleotide sequences.1.3 http://purl.bioontology.org/ontology/MSH/D019175 1.1 - + @@ -48879,11 +49626,12 @@ positional features such as functional sites in nucleotide sequences. - Structural variation + DNA structural variation 1.1 Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. + Structural variation Genomic structural variation @@ -48896,6 +49644,7 @@ positional features such as functional sites in nucleotide sequences. DNA packaging + Nucleosome positioning beta12orEarlier DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. http://purl.bioontology.org/ontology/MSH/D042003 @@ -48941,14 +49690,14 @@ positional features such as functional sites in nucleotide sequences. ChIP-on-chip + - true - 1.3 + ChiP + ChIP-Chip 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 - - + @@ -49024,9 +49773,10 @@ positional features such as functional sites in nucleotide sequences.Epigenetics Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. - DNA methylation - This includes sub-topics such as histone modification and DNA methylation. + This includes sub-topics such as histone modification and DNA methylation. DNA methylation includes bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. http://purl.bioontology.org/ontology/MSH/D019175 + DNA methylation + Bisulfite sequencing Histone modification 1.3 @@ -49056,6 +49806,7 @@ positional features such as functional sites in nucleotide sequences.Phenomics + 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 @@ -49199,8 +49950,7 @@ positional features such as functional sites in nucleotide sequences. Computational biology - - + 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). @@ -49223,9 +49973,11 @@ positional features such as functional sites in nucleotide sequences.Transcriptomics + Metatranscriptomics The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. Transcriptome 1.3 + Comparative transcriptomics @@ -49319,6 +50071,7 @@ positional features such as functional sites in nucleotide sequences.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 + Alternative splicing @@ -49578,8 +50331,7 @@ positional features such as functional sites in nucleotide sequences. Biomedical science - - + Topic concerning biological science that is (typically) performed in the context of medicine. VT 3.3 Health sciences Health science @@ -49609,12 +50361,14 @@ positional features such as functional sites in nucleotide sequences. Sequence search - + 1.3 Sequence database search + true + 1.12 The search and retrieval from a database on the basis of molecular sequence similarity. - - + + @@ -49875,9 +50629,12 @@ positional features such as functional sites in nucleotide sequences. Preclinical and clinical studies + 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 study + Preclinical study Clinical studies @@ -50015,7 +50772,7 @@ positional features such as functional sites in nucleotide sequences. Omics - + 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 @@ -50122,9 +50879,9 @@ positional features such as functional sites in nucleotide sequences. 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 - Aging + Ageing Gerontology + Aging 1.4 Geriatrics @@ -50695,6 +51452,7 @@ positional features such as functional sites in nucleotide sequences. Nucleic acid features (mRNA features) + Fusion transcripts 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). @@ -50748,7 +51506,7 @@ positional features such as functional sites in nucleotide sequences. GWAS study - + 1.8 Genome-wide association study experiments. Genome-wide association study @@ -50763,9 +51521,23 @@ positional features such as functional sites in nucleotide sequences. Microarray experiment + ChIP-chip + Microarray experiments including conditions, protocol, sample:data relationships etc. + Microarrays + Tissue microarray + Reverse phase protein array + Methylation array + mRNA microarray + Multichannel microarray + Proprietary platform micoarray + MicroRNA array 1.8 + Two channel microarray + miRNA array 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. + One channel microarray + ChIP-on-chip + Genotyping array @@ -50828,7 +51600,7 @@ positional features such as functional sites in nucleotide sequences. RNAi experiment - + 1.8 RNAi experiments. @@ -51127,6 +51899,23 @@ positional features such as functional sites in nucleotide sequences. + + + Protein interaction experiment + + 1.12 + Yeast one-hybrid + Co-immunoprecipitation + An experiment for studying protein-protein interactions. + Yeast two-hybrid + Phage display + + + + + + @@ -51269,6 +52058,108 @@ positional features such as functional sites in nucleotide sequences. + + + Immunoprecipitation experiment + + + + Chromatin immunoprecipitation + Experimental techniques to purify a protein-DNA crosslinked complex. Usually sequencing follows e.g. in the techniques ChIP-chip, ChIP-seq and MeDIP-seq. + 1.12 + + + + + + + + + + Whole genome sequencing + + 1.12 + Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time. + WGS + Whole genome resequencing + + + + + + + + + + Methylated DNA immunoprecipitation + + 1.12 + MeDIP-seq + Methylated DNA immunoprecipitation (MeDIP) + Methylation sequencing + Laboratory technique to sequence the methylated regions in DNA. + MeDIP-chip + Bisulfite sequencing + MeDIP + mDIP + + + + + + + + + + Exome sequencing + + 1.1 + Exome capture + Exome sequencing is considered a cheap alternative to whole genome sequencing. + Targeted exome capture + Exome sequence analysis + Laboratory technique to sequence all the protein-coding regions in a genome, i.e., the exome. + Exome analysis + + + + + + + + + + + Experimental design and studies + + Design of experiments + 1.12 + Experimental design + Studies + The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions. + + + + + + + + + + + Animal study + + + Challenge study + 1.12 + The design of an experiment involving non-human animals. + + + + + +