19:06:2014 15:41 EDAM EDAM http://edamontology.org/ "EDAM relations and concept properties" EDAM_topic http://edamontology.org/topic_ "EDAM topics" Jon Ison application/rdf+xml BioMedical Topics : an ontology of biological and biomedical topics, created from merging the EDAM Topics sub-ontology with auxiliary topics that are out of scope of EDAM. 1.4 concept_properties "EDAM concept properties" relations "EDAM relations" topics "EDAM topics" Jon Ison true Version in which a concept was created. concept_properties Created in true 'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format. Specification concept_properties Documentation true 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. concept_properties Example true Version in which a concept was made obsolete. concept_properties Obsolete since true 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. concept_properties Regular expression false false false OBO_REL:is_a 'A has_format B' defines for the subject A, that it has the object B as its data format. bioinformatics edam relations false Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. has format 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject. false false false OBO_REL:is_a 'A has_function B' defines for the subject A, that it has the object B as its function. OBO_REL:bearer_of bioinformatics edam relations true Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. has function 'OBI:has_function' only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes, with objects that are a 'function' (snap:Function). It does not define explicitly that the object is a function of the subject. OBO_REL:bearer_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. true In very unusual cases. false false false OBO_REL:is_a 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. bioinformatics edam relations false Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. has identifier false false false OBO_REL:is_a 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument. OBO_REL:has_participant bioinformatics edam relations true Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. has input 'OBI:has_specified_input' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). 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. true In very unusual cases. false false false OBO_REL:is_a 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. OBO_REL:has_participant bioinformatics edam relations true Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. has output true In very unusual cases. 'OBI:has_specified_output' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). OBO_REL:has_participant 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. false false false OBO_REL:is_a 'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B). bioinformatics edam relations true Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. has topic 'ao:hasTopic' is narrower in the sense that it only relates subjects that are an annotation, and it is broader in the sense that it relates with any resource. 'is about' is narrower in the sense that it only relates subjects that are information artifacts and the relation is not necessarily the one of having a topic. It is broader in the sense that it relates with any object. 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject. true In very unusual cases. false false false OBO_REL:is_a 'A is_format_of B' defines for the subject A, that it is a data format of the object B. OBO_REL:quality_of bioinformatics edam relations false Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. is format of 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. false false false OBO_REL:is_a 'A is_function_of B' defines for the subject A, that it is a function of the object B. OBO_REL:function_of OBO_REL:inheres_in bioinformatics edam relations true Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used. is function of 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: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. true In very unusual cases. false false false OBO_REL:is_a 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B. bioinformatics edam relations false Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined. is identifier of false false false OBO_REL:is_a 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. OBO_REL:participates_in bioinformatics edam relations true Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'. is input of 'OBI:is_specified_input_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). OBO_REL:participates_in 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. true In very unusual cases. false false false OBO_REL:is_a 'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B. OBO_REL:participates_in bioinformatics edam relations true Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. is output of 'OBI:is_specified_output_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). 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. true In very unusual cases. false false false OBO_REL:is_a 'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B). OBO_REL:quality_of bioinformatics edam relations true Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. is topic of 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. edamontology:topic_0077 beta12orEarlier topic Topic concerning the processing and analysis of nucleic acid sequence, structural and other data. Nucleic acid analysis Nucleic acid bioinformatics Nucleic acid informatics Nucleic acid physicochemistry Nucleic acid properties Nucleic acids edamontology:topic_0078 beta12orEarlier topic Topic concerning archival, processing and analysis of protein data, typically molecular sequence and structural data. Protein analysis Protein bioinformatics Protein informatics Protein databases Proteins edamontology:topic_0079 beta12orEarlier topic Topic concerning the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. Metabolite structures This concept excludes macromolecules such as proteins and nucleic acids. Metabolites edamontology:topic_0080 beta12orEarlier topic BioCatalogue:Sequence Analysis Topic concerning the archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles. Sequences Sequence databases Sequence analysis edamontology:topic_0081 beta12orEarlier topic Topic concerning the curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. Structural bioinformatics Structure analysis Computational structural biology Structure data resources Structure databases This includes related concepts such as structural properties, alignments and structural motifs. Structure analysis edamontology:topic_0082 beta12orEarlier topic Topic concerning the prediction of molecular (secondary or tertiary) structure. Structure prediction edamontology:topic_0084 beta12orEarlier topic BioCatalogue:Evolutionary Distance Measurements BioCatalogue:Phylogeny BioCatalogue:Statistical Robustness BioCatalogue:Tree Inference Topic concerning the study of evolutionary relationships amongst organisms. Phylogenetic clocks Phylogenetic dating Phylogenetic simulation Phylogenetic stratigraphy Phylogeny reconstruction This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc. Phylogeny edamontology:topic_0085 beta12orEarlier topic BioCatalogue:Functional Genomics Topic concerning the study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. Functional genomics edamontology:topic_0089 beta12orEarlier topic BioCatalogue:Ontology BioCatalogue:Ontology Lookup Topic concerning the conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource. Applied ontology Ontologies Ontology Terminology Ontology and terminology edamontology:topic_0090 beta12orEarlier topic BioCatalogue:Data Retrieval BioCatalogue:Identifier Retrieval BioCatalogue:Image Retrieval BioCatalogue:Sequence Retrieval BioCatalogue:Structure Retrieval Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information. Data query Data retrieval Data search This includes, for example, search, query and retrieval of molecular sequences and associated data. Data search, query and retrieval edamontology:topic_0091 beta12orEarlier topic Topic concerning the archival, curation, processing and analysis of complex biological data. This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation. Bioinformatics edamontology:topic_0092 beta12orEarlier topic Topic for the plotting or rendering (drawing on a computer screen) of molecular sequences, structures or other biomolecular data. Data plotting Data rendering Data rendering and visualisation Data visualisation edamontology:topic_0097 beta12orEarlier topic Topic concerning the archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. Nucleic acid structure DNA melting Nucleic acid denaturation Nucleic acid thermodynamics RNA alignment RNA structure RNA structure alignment Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc. Nucleic acid structure analysis edamontology:topic_0099 beta12orEarlier topic Topic concerning RNA sequences and structures. RNA edamontology:topic_0102 beta12orEarlier topic Topic concerning the mapping of complete (typically nucleotide) sequences. Genetic linkage Linkage Linkage 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. Mapping edamontology:topic_0108 beta12orEarlier topic Topic concerning the translation of mRNA into protein and subsequent protein processing in the cell. Translation Protein expression edamontology:topic_0114 beta12orEarlier topic Topic concerning resources that aim to identify, predict, model, analyse or curate gene structure in DNA sequences. This includes introns, exons, and gene fusion. This includes the study of promoters, coding regions etc. Gene structure edamontology:topic_0121 beta12orEarlier topic BioCatalogue:Proteomics Topic concerning protein and peptide identification, especially in the study of whole proteomes of organisms. Peptide identification Protein and peptide identification Protein expression Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues. Proteomics edamontology:topic_0122 beta12orEarlier topic BioCatalogue:Structural Genomics Topic concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism. Structural genomics edamontology:topic_0123 beta12orEarlier topic Topic concerning the study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein. Protein physicochemistry Protein hydropathy Protein properties edamontology:topic_0128 beta12orEarlier topic BioCatalogue:Ligand Interaction BioCatalogue:Protein Interaction Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. Protein-DNA interaction Protein-RNA interaction Protein-ligand interactions Protein-nucleic acid interactions Protein-protein interactions This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. Protein interactions edamontology:topic_0130 beta12orEarlier topic Topic concerning protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. Protein design Protein folding Protein residue interactions Protein stability Rational protein design Protein folding, stability and design edamontology:topic_0134 beta12orEarlier Topic concerning an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. Mass spectrometry edamontology:topic_0140 beta12orEarlier topic Topic concerning the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. Protein localization Protein sorting Protein targeting Protein targeting and localization edamontology:topic_0152 beta12orEarlier topic Topic concerning carbohydrates, typically including structural information. Carbohydrates edamontology:topic_0153 beta12orEarlier topic Topic concerning lipids and their structures. Lipids edamontology:topic_0154 beta12orEarlier topic Topic concerning small molecules of biological significance, typically archival, curation, processing and analysis of structural information. CHEBI:23367 Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. Small molecules edamontology:topic_0157 beta12orEarlier topic BioCatalogue:Repeats Topic concerning the archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences. Low complexity sequences Repeat sequences Sequence complexity Sequence composition Sequence repeats Sequence composition, complexity and repeats edamontology:topic_0159 beta12orEarlier topic BioCatalogue:Nucleotide Sequence Similarity BioCatalogue:Protein Sequence Similarity Topic concerning the comparison of two or more molecular sequences. The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. Sequence comparison edamontology:topic_0160 beta12orEarlier topic Topic concerning the archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. Functional sites HMMs Protein functional sites Protein sequence features Sequence feature detection Sequence features Sequence motifs Sequence profiles Sequence sites Sequence sites, features and motifs edamontology:topic_0164 beta12orEarlier topic Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities. Sequence clusters This includes systems that generate, process and analyse sequence clusters. Sequence clustering edamontology:topic_0166 beta12orEarlier topic Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. Protein structural features Protein structural motifs Protein surfaces Structural motifs This includes solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches and so on. Protein structural motifs and surfaces edamontology:topic_0172 beta12orEarlier topic BioCatalogue:Protein Structure Prediction Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. Protein structure prediction edamontology:topic_0173 beta12orEarlier topic BioCatalogue:Nucleotide Secondary Structure BioCatalogue:Nucleotide Structure Prediction BioCatalogue:Nucleotide Tertiary Structure Topic concerning the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. RNA structure prediction DNA structure prediction Nucleic acid design Nucleic acid folding Nucleic acid structure prediction edamontology:topic_0174 beta12orEarlier topic Topic concerning the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates. de novo protein structure prediction Ab initio structure prediction edamontology:topic_0176 beta12orEarlier topic Molecular flexibility Molecular motions Topic concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. This includes resources concerning flexibility and motion in protein and other molecular structures. Molecular dynamics edamontology:topic_0177 beta12orEarlier topic Topic concerning the modelling the structure of proteins in complex with small molecules or other macromolecules. Molecular docking edamontology:topic_0180 beta12orEarlier topic Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). For example threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). Protein fold recognition edamontology:topic_0182 beta12orEarlier topic BioCatalogue:Nucleotide Multiple Alignment BioCatalogue:Nucleotide Pairwise Alignment BioCatalogue:Nucleotide Sequence Alignment BioCatalogue:Protein Multiple Alignment BioCatalogue:Protein Pairwise Alignment BioCatalogue:Protein Sequence Alignment Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments). This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. Sequence alignment edamontology:topic_0183 beta12orEarlier topic Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). Structure alignment generation This includes the generation, storage, analysis, rendering etc. of structure alignments. Structure alignment edamontology:topic_0194 beta12orEarlier topic Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. Phylogenomics edamontology:topic_0196 beta12orEarlier topic Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence. Assembly This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. Sequence assembly edamontology:topic_0199 beta12orEarlier topic Topic concerning DNA sequence variation (mutation and polymorphism) data. DNA variation Mutation Polymorphism Genetic variation edamontology:topic_0202 beta12orEarlier topic Topic concerning the study of drugs and their effects or responses in living systems. Computational pharmacology Pharmacoinformatics Pharmacology edamontology:topic_0203 beta12orEarlier topic http://edamontology.org/topic_0197 BioCatalogue:Microarrays Topic concerning the analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. Gene expression analysis Codon usage DNA microarrays Expression profiling Gene expression profiling Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc. Gene expression edamontology:topic_0204 beta12orEarlier topic Topic concerning primarily the regulation of gene expression. Gene regulation edamontology:topic_0208 beta12orEarlier topic Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. Pharmacogenomics edamontology:topic_0209 beta12orEarlier topic Topic concerning the design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes. Drug design This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. Medicinal chemistry edamontology:topic_0218 beta12orEarlier topic Literature analysis BioCatalogue:Document Clustering BioCatalogue:Document Similarity BioCatalogue:Named Entity Recognition BioCatalogue:Text Mining Topic concerning the analysis of the biomedical and informatics literature. Literature mining Text data mining Text mining edamontology:topic_0219 beta12orEarlier topic BioCatalogue:Genome Annotation BioCatalogue:Ontology Annotation Topic concerning the organisation and maintenance of a collection of biological database entries (or other such entities) and their annotation, typically with terms from a controlled vocabulary. Annotation Curation Genome annotation Ontology annotation Data curation and annotation edamontology:topic_0220 beta12orEarlier topic Topic concerning basic manipulations of files or reports of generic biological data. Data file handling File handling Report handling Report processing Data types Datatypes This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. Data processing and validation edamontology:topic_0593 beta12orEarlier Spectroscopy Topic concerning an analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. NMR Nuclear magnetic resonance spectroscopy NMR spectroscopy edamontology:topic_0594 beta12orEarlier topic Topic concerning 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. Sequence classification edamontology:topic_0601 beta12orEarlier topic Topic concerning protein chemical modifications, e.g. post-translational modifications. Protein post-translational modification GO:0006464 MOD:00000 EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) Protein modifications edamontology:topic_0602 beta13 topic http://edamontology.org/topic_3076 BioCatalogue:Pathway Retrieval BioCatalogue:Pathways Topic concerning molecular interactions, biological pathways, networks and other models. Biological models Biological networks Biological pathways Molecular interactions Network or pathway analysis Molecular interactions, pathways and networks edamontology:topic_0607 beta12orEarlier topic Topic concerning laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. Laboratory resources Laboratory information management edamontology:topic_0610 beta12orEarlier topic Environmental science Topic concerning the ecological and environmental sciences and especially the application of information technology (ecoinformatics). Computational ecology Ecoinformatics Ecological informatics Ecology edamontology:topic_0611 beta12orEarlier Topic concerning the use of electrons to analyse structures at resolutions higher than can be achieved using light. Electron microscopy edamontology:topic_0613 beta12orEarlier topic Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides. Amino acids Peptides Peptides and amino acids edamontology:topic_0620 beta12orEarlier topic Topic concerning the structures of drugs, drug target, their interactions and binding affinities. Drug structures Target structures Drugs and target structures edamontology:topic_0621 beta12orEarlier topic Topic concerning a specific organism, or group of organisms, used to study a particular aspect of biology. Model organisms This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism. Organisms edamontology:topic_0622 beta12orEarlier topic BioCatalogue:Genomics Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. Genomics edamontology:topic_0623 beta12orEarlier topic Topic concerning particular gene(s), gene family or other gene group or system and their encoded proteins. Gene and protein families Gene family Gene system Genes, gene family or system Gene families edamontology:topic_0624 beta12orEarlier topic Topic concerning chromosomes. Chromosomes edamontology:topic_0625 beta12orEarlier topic Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. Genotype and phenotype resources Genotyping Genotype and phenotype edamontology:topic_0632 beta12orEarlier topic Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR). Gene design Primer design Primers Probe design Probes in silico cloning This includes the design of primers for PCR and DNA amplification or the design of molecular probes. Sequence design edamontology:topic_0634 beta12orEarlier topic Topic concerning diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. Diseases Pathology edamontology:topic_0639 beta12orEarlier topic BioCatalogue:Protein Sequence Analysis Topic concerning archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. Protein sequences Protein sequence analysis edamontology:topic_0640 beta12orEarlier topic BioCatalogue:Nucleotide Sequence Analysis Topic concerning the archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. Nucleic acid sequence analysis edamontology:topic_0654 beta12orEarlier topic Topic concerning DNA sequences and structure, including processes such as methylation and replication. DNA analysis The DNA sequences might be coding or non-coding sequences. DNA edamontology:topic_0655 beta12orEarlier topic Topic concerning messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences. EST cDNA mRNA Coding RNA edamontology:topic_0659 beta12orEarlier topic Topic concerning non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). Functional RNA Non-coding RNA 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). Functional, regulatory and non-coding RNA edamontology:topic_0694 beta12orEarlier topic BioCatalogue:Protein Secondary Structure Topic concerning protein secondary structure or secondary structure alignments. Protein secondary structure analysis This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. Protein secondary structure edamontology:topic_0698 beta12orEarlier topic BioCatalogue:Protein Tertiary Structure Topic concerning protein tertiary structures. Protein tertiary structure analysis Protein tertiary structure edamontology:topic_0724 beta12orEarlier topic Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group. Protein secondary databases Protein sequence classification A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. Protein families edamontology:topic_0736 beta12orEarlier topic BioCatalogue:Domains Topic concerning protein tertiary structural domains and folds. Protein domains Protein folds Protein domains and folds edamontology:topic_0749 beta12orEarlier topic BioCatalogue:Transcription Factors Topic concerning proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. Transcription factor binding sites Transcription factors Transcriptional 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. Transcription factors and regulatory sites edamontology:topic_0753 beta12orEarlier topic Topic concerning metabolic pathways. Metabolic pathways edamontology:topic_0754 beta12orEarlier topic Topic concerning signaling pathways. Signaling pathways edamontology:topic_0780 beta12orEarlier topic Botany Plant biology Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. Plant The resource may be specific to a plant, a group of plants or all plants. Plants edamontology:topic_0781 beta12orEarlier topic Virology Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. The resource may be specific to a virus, a group of viruses or all viruses. Viruses edamontology:topic_0782 beta12orEarlier topic Mycology Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. The resource may be specific to a fungus, a group of fungi or all fungi. Fungi edamontology:topic_0783 beta12orEarlier topic Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. The resource may be specific to a pathogen, a group of pathogens or all pathogens. Pathogens edamontology:topic_0797 beta12orEarlier topic BioCatalogue:Comparative Genomics Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes. Comparative genomics edamontology:topic_0798 beta12orEarlier topic Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. Mobile genetic elements edamontology:topic_0804 beta12orEarlier topic Topic concerning the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. Computational immunology Immunoinformatics Immunology edamontology:topic_0820 beta12orEarlier topic Topic concerning lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. Lipoproteins Membrane proteins Transmembrane proteins Membrane and lipoproteins edamontology:topic_0821 beta12orEarlier topic Topic concerning proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. Enzymology Enzymes edamontology:topic_1317 1.3 topic This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy. Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen. Topic concerning the molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. Structural assignment Structural determination Structure determination This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. Structural biology edamontology:topic_1770 beta12orEarlier topic Topic concerning the comparison of two or more molecular structures. This might involve comparison of secondary or tertiary (3D) structural information. Structure comparison edamontology:topic_1775 beta12orEarlier topic BioCatalogue:Function Prediction Topic concerning the study of gene and protein function including the prediction of functional properties of a protein. Protein function analysis Protein function prediction Function analysis edamontology:topic_1811 beta12orEarlier topic Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation. The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. Prokaryotes and archae edamontology:topic_2229 beta12orEarlier topic Topic concerning cells, such as key genes and proteins involved in the cell cycle. Cell biology edamontology:topic_2258 beta12orEarlier topic BioCatalogue:Chemoinformatics Topic concerning the application of information technology to chemistry in biological research environment. Chemical informatics Chemoinformatics Cheminformatics edamontology:topic_2259 beta12orEarlier topic BioCatalogue:Model Analysis BioCatalogue:Model Creation BioCatalogue:Model Execution BioCatalogue:Systems Biology Topic concerning the holistic modelling and analysis of complex biological systems and the interactions therein. Biological modelling Biological models Biological system modelling This includes databases of models and methods to construct or analyse a model. Systems biology edamontology:topic_2269 beta12orEarlier topic BioCatalogue:Biostatistics Topic concerning the application of statistical methods to biological problems. Biostatistics Statistics edamontology:topic_2275 beta12orEarlier topic Topic concerning the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. Molecular modeling Comparative modeling Comparative modelling Homology modeling Homology modelling Molecular modelling edamontology:topic_2277 beta12orEarlier topic Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. SNPs edamontology:topic_2640 beta12orEarlier topic Topic concerning the study of cancer, for example, genes and proteins implicated in cancer. Cancer biology Cancer Oncology edamontology:topic_2661 beta12orEarlier topic Topic concerning structural and associated data for toxic chemical substances. Targets Toxins Toxins and targets edamontology:topic_2814 beta12orEarlier topic http://edamontology.org/topic_3040 Topic concerning protein secondary or tertiary structural data and/or associated annotation. Protein structure Protein structure analysis edamontology:topic_2818 beta12orEarlier topic Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation. Eukaryote The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. Eukaryotes edamontology:topic_2819 beta12orEarlier topic Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation. The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. Invertebrates edamontology:topic_2820 beta12orEarlier topic Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. Vertebrates edamontology:topic_2821 beta12orEarlier topic Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation. The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. Unicellular eukaryotes edamontology:topic_2828 beta12orEarlier Topic concerning the study of crystals and their structure by means of the diffraction of X-rays by the regularly spaced atoms of crystalline materials. Crystallography X-ray crystallography edamontology:topic_2830 beta12orEarlier topic Topic concerning immunity-related genes, proteins and their ligands. Antigens Immunogenes Immunopeptides Immunoproteins This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." Immunoproteins, genes and antigens edamontology:topic_2840 beta12orEarlier topic Toxicology Topic concerning toxins and the adverse effects of these chemical substances on living organisms. Computational toxicology Toxicoinformatics Toxicology edamontology:topic_2844 beta12orEarlier topic Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters. Structure classification Structural clustering edamontology:topic_2846 beta12orEarlier topic Topic concerning gene regulatory networks. Gene regulatory networks edamontology:topic_3047 beta13 topic Topic concerning the molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. Molecular biology edamontology:topic_3050 beta13 topic Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet. Biodiversity edamontology:topic_3053 beta13 topic Topic concerning the study of genes, genetic variation and heredity in living organisms. Genetics data resources Gene database Gene resource Genetics edamontology:topic_3055 beta13 topic Topic concerning the genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). Quantitative genetics edamontology:topic_3056 beta13 topic Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. Population genetics edamontology:topic_3061 beta13 topic Topic concerning the documentation of resources such as tools, services and databases and how to get help. Documentation Help Documentation and help edamontology:topic_3063 beta13 topic Molecular medicine Translational medicine Topic concerning the application of information technology to health, disease and biomedicine. Biomedical informatics Clinical informatics Health and disease Health informatics Healthcare informatics Medical informatics edamontology:topic_3064 beta13 topic Topic concerning how organisms grow and develop. Developmental biology edamontology:topic_3065 beta13 topic Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. Embryology edamontology:topic_3067 beta13 topic Topic concerning the form and function of the structures of living organisms. Anatomy edamontology:topic_3068 beta13 topic Topic concerning the scientific literature, reference information and documentation. Literature search Literature sources Literature and reference edamontology:topic_3070 beta13 topic Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on. Biological science Biology edamontology:topic_3071 beta13 topic Topic concerning the general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. Databases Data handling Databases Knowledge management Data management edamontology:topic_3077 beta13 topic Topic concerning the acquisition and deposition of biological data. Database submission Data acquisition Data deposition Deposition Data acquisition and deposition edamontology:topic_3168 1.1 topic Topic concerning 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 Next generation sequencing Sequencing edamontology:topic_3172 1.1 topic Topic concerning the systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism. Metabolomics edamontology:topic_3173 1.1 topic Topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc. Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. Epigenomics edamontology:topic_3174 1.1 topic Community genomics Ecogenomics Environmental genomics Topic concerning the study of genetic material recovered from environmental samples, and associated environmental data. Metagenomics edamontology:topic_3175 1.1 topic Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. Genomic structural variation Structural variation edamontology:topic_3176 beta12orEarlier topic Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. DNA packaging edamontology:topic_3263 1.3 topic Security Topic concerning the protection of data, for example, patient health data. Privacy Security Data security edamontology:topic_3277 1.3 topic Topic concerning biological samples and specimens. Specimen collections biobanking biosamples samples Sample collections edamontology:topic_3292 1.3 topic Topic concerning chemical substances and physico-chemical processes and that occur within living organisms. Biological chemistry Chemical biology Biochemistry edamontology:topic_3293 1.3 topic Topic concerning the study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). Phylogenetics edamontology:topic_3295 1.3 topic DNA methylation Histone modification Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. This includes sub-topics such as histone modification and DNA methylation. Epigenetics edamontology:topic_3297 1.3 topic Topic concerning the exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. Biotechnology edamontology:topic_3298 1.3 topic Topic concerning phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. Phenomics edamontology:topic_3299 1.3 topic Topic concerning the evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. Evolutionary biology edamontology:topic_3300 1.3 topic Topic concerning the functions of living organisms and their constituent parts. Physiology edamontology:topic_3301 1.3 topic Topic concerning the biology of microorganisms. Microbiology edamontology:topic_3302 1.3 topic Topic concerning the biology of parasites. Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. Parasitology edamontology:topic_3303 1.3 topic Topic concerning research in support of healing by diagnosis, treatment, and prevention of disease. Biomedical research Experimental medicine Medicine edamontology:topic_3304 1.3 topic Neuroscience Topic concerning the study of the nervous system and brain; its anatomy, physiology and function. Neurobiology edamontology:topic_3305 1.3 topic Topic concerning the the patterns, cause, and effect of disease within populations. Epidemiology Public health Public health and epidemiology edamontology:topic_3306 1.3 topic Topic concerning the use of physics to study biological system. Biophysics edamontology:topic_3307 1.3 topic BioCatalogue:Model Execution Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. Biomathematics Mathematical biology Theoretical biology This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology). Computational biology edamontology:topic_3308 1.3 topic Topic concerning the analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. Transcriptome Transcriptomics edamontology:topic_3314 1.3 topic Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances. Chemistry edamontology:topic_3315 1.3 topic Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances. Maths Mathematics edamontology:topic_3316 1.3 topic Topic concerning the theory and practical use of computer systems. Computer science edamontology:topic_3318 1.3 topic Topic concerning the study of matter, space and time, and related concepts such as energy and force. Physics edamontology:topic_3320 1.3 topic Topic concerning 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. RNA splicing edamontology:topic_3321 1.3 topic Topic concerning the structure and function of genes at a molecular level. Molecular genetics edamontology:topic_3322 1.3 topic Topic concerning the study of respiratory system. Pulmonary medicine Pulmonology Pulmonary disorders Respiratory disease Respiratory medicine edamontology:topic_3324 1.3 topic Topic concerning the branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions). Communicable disease Transmissable disease Infectious disease edamontology:topic_3325 1.3 topic Topic concerning the study of rare diseases. Rare diseases edamontology:topic_3332 1.3 topic Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. Computational chemistry edamontology:topic_3334 1.3 topic Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. Neurological disorders Neurology edamontology:topic_3335 1.3 topic Topic concerning the diseases and abnormalities of the heart and circulatory system. Cardiovascular medicine Cardiovascular disease Heart disease Cardiology edamontology:topic_3336 1.3 topic Topic concerning the discovery and design of drugs or potential drug compounds. This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. Drug discovery edamontology:topic_3337 1.3 topic Topic concerning repositories of biological samples, typically human, for basic biological and clinical research. Tissue collection biobanking Biobank edamontology:topic_3338 1.3 topic Topic concerning laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. Mouse clinic edamontology:topic_3339 1.3 topic Topic concerning collections of microbial cells including bacteria, yeasts and moulds. Microbial collection edamontology:topic_3340 1.3 topic Topic concerning collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells. Cell culture collection edamontology:topic_3341 1.3 topic Topic concerning collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. Clone library edamontology:topic_3342 1.3 topic Topic concerning 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. Translational medicine edamontology:topic_3343 1.3 topic Translational medicine Topic concerning collections of chemicals, typically for use in high-throughput screening experiments. Chemical library Chemical screening Compound library Compound libraries and screening edamontology:topic_3344 1.3 topic Topic concerning biological science that is (typically) performed in the context of medicine. Biomedical science edamontology:topic_3345 1.3 topic Topic concerning the identity of biological data and the mapping of entities in different databases. Data identity and mapping edamontology:topic_3346 1.3 topic Topic concerning the search and retrieval from a database on the basis of molecular sequence similarity. Sequence database search Sequence search edamontology:topic_3360 1.4 Topic concerning objective indicators of biological state often used to assess health, and determinate treatment. Diagnostic markers Biomarkers edamontology:topic_3361 1.4 Topic concerning the procedures used to conduct an experiment. Lab techniques Laboratory techniques edamontology:topic_3362 1.4 Topic concerning the application of scientific knowledge for practical purposes. Technology edamontology:topic_3363 1.4 Topic concerning the study of thought, learning, and mental organisation, which draws on aspects of psychology, linguistics, philosophy and computer modelling. Lab techniques Cognitive science edamontology:topic_3364 1.4 Topic concerning the transferable skills needed by an individual to make them 'employable' in addition to good technical understanding and subject knowledge. Employability skills Key competencies Transferable skills This entire branch will probably be hived off into it's own module. Kept here for now as a convenience for annotators. Auxiliary skills edamontology:topic_3365 1.4 Topic concerning the process of systematically applying statistical and / or logical techniques to describe and illustrate, condense and recap, and evaluate data. Data analysis edamontology:topic_3366 1.4 Topic concerning the combination of data from different sources to provide users with a unified view of these data. Data integration edamontology:topic_3367 1.4 Topic concerning the discovery and design of new materials. Materials engineering Material science edamontology:topic_3368 1.4 Topic concerning any matter, surface or construct that interacts with a biological system. Diagnostic markers Biomaterials edamontology:topic_3369 1.4 Topic concerning the use of synthetic chemistry to study and manipulate biological systems. Chemical biology edamontology:topic_3370 1.4 Topic concerning the study of the separation, identification, and quantification of the chemical components of natural and artificial materials. Analytical chemistry edamontology:topic_3371 1.4 Topic concerning the use of chemistry to create new compounds. Synthetic organic chemistry Synthetic chemistry edamontology:topic_3372 1.4 Topic concerning the process that leads from an original formulation of a computing problem to executable programs. Software development Computer programming edamontology:topic_3373 1.4 Topic concerning the process of bringing a new drug to market once a lead compounds has been identified through drug discovery. Drug development science Medicine development Medicines development Drug development edamontology:topic_3374 1.4 Topic concerning the process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. Drug delivery Drug formulation Drug formulation and delivery edamontology:topic_3375 1.4 Drug metabolism Topic concerning the study of how a drug interacts with the body. ADME Drug absorption Drug distribution Drug excretion Drug metabolism Pharmacodynamics Pharmacokinetics Pharmacokinetics and pharmacodynamics edamontology:topic_3376 1.4 Health care research Topic concerning the discovery, development and approval of medicines. Drug discovery and development Medicines research and development edamontology:topic_3377 1.4 Topic concerning the safety (or lack) of drugs and other medical interventions. Drug safety Safety sciences edamontology:topic_3378 1.4 Topic concerning the detection, assesment, understanding and prevention of adverse effects of medicines. Pharmacovigilence concerns safety once a drug has gone to market. Pharmacovigilence edamontology:topic_3379 1.4 Topic concerning the testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities. Clinical studies Preclinical studies Preclinical and clinical studies edamontology:topic_3380 1.4 Topic concerning intangible property that is the result of creativity, such as patents and copyrights. IP IPR Intellectual property rights Copyrights Patents Intellectual property edamontology:topic_3381 1.4 Topic concerning the branch of economics concerned with issues related to efficiency, effectiveness, value and behaviour in the production and consumption of health care. Health economics edamontology:topic_3382 1.4 Topic concerning the visual representation of an object. Microscopy Imaging edamontology:topic_3383 1.4 Topic concerning the use of imaging techniques to understand biology. Biological imaging edamontology:topic_3384 1.4 Topic concerning the use of imaging techniques for clinical purposes for medical research. Medical imaging edamontology:topic_3385 1.4 Topic concerning the use of optical instruments to magnify the image of an object. Light microscopy edamontology:topic_3386 1.4 Topic concerning the use of animals and alternatives in experimental research. Laboratory animal science edamontology:topic_3387 1.4 Topic concerning the study of organisms in the ocean or brackish waters. Marine biology edamontology:topic_3388 1.4 Topic concerning the identification of molecular and genetic causes of disease and the development of interventions to correct them. Molecular medicine edamontology:topic_3389 1.4 Nanoscience Topic concerning the manipulation of matter at an atomic level. Nanotechnology edamontology:topic_3390 1.4 Topic concerning the study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices. Nutrition science Nutritional science edamontology:topic_3391 1.4 Topic concerning the collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. Omics edamontology:topic_3392 1.4 Topic concerning the scientific study of the human mind. Psychology edamontology:topic_3393 1.4 Topic concerning the processes that need to be in place to ensure the quality of products for human or animal use. Quality assurance Good clinical practice Good laboratory practice Good manufacturing practice Quality affairs edamontology:topic_3394 1.4 Topic concerning the protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines. Regulatory affairs edamontology:topic_3395 1.4 Topic concerning biomedical approaches to clinical interventions that involve the use of stem cells. Stem cell research Regnerative medicine edamontology:topic_3396 1.4 Topic concerning an interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life. Systems medicine edamontology:topic_3397 1.4 Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals. Veterinary medicine edamontology:topic_3398 1.4 Topic concerning the application of biological concepts and methods to the analytical and synthetic methodologies of engineering. Diagnostic markers Bioengineering edamontology:topic_3399 1.4 Topic concerning the branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. Ageing Aging Geriatrics Geriatric medicine edamontology:topic_3400 1.4 Topic concerning health issues related to the immune system and their prevention, diagnosis and mangement. Allergy Clinical immunology Immune disorders Immunomodulators Immunotherapeutics Allergy, clinical immunology and immunotherapeutics. edamontology:topic_3401 1.4 Topic concerning with the prevention of pain and the evaluation, treatment and rehabilitation of persons in pain. Ageing Algiatry Pain medicine edamontology:topic_3402 1.4 Topic concerning anaesthesia and anaesthetics. Anaesthetics Anaesthesiology edamontology:topic_3403 1.4 Topic concerning the multidisciplinary that cares for patients with acute, life-threatening illness or injury. Acute medicine Emergency medicine Geriatrics Critical care medicine edamontology:topic_3404 1.4 Topic concerning the branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails. Dermatological disorders Dermatology edamontology:topic_3405 1.4 Topic concerning the study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures. Dentistry edamontology:topic_3406 1.4 Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat. Audiovestibular medicine Otolaryngology Head and neck disorders Ear, nose and throat medicine edamontology:topic_3407 1.4 Topic concerning the branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism. Endocrine disorders Endocrinology Metabolic disorders Metabolism Endocrinology and metabolism edamontology:topic_3408 1.4 Topic concerning the branch of medicine that deals with the blood, blood-forming organs and blood diseases. Blood disorders Haematological disorders Haematology edamontology:topic_3409 1.4 Topic concerning the branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum. Gastrointestinal disorders Gastroenterology edamontology:topic_3410 1.4 Topic concerning the study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management. Gender medicine edamontology:topic_3411 1.4 Topic concerning the branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. Gynaecological disorders Gynaecology Obstetrics Gynaecology and obstetrics edamontology:topic_3412 1.4 Topic concerning the branch of medicine that deals with the liver, gallbladder, bile ducts and bile. Hepatobiliary medicine Liver disorders Hepatic and biliary medicine edamontology:topic_3413 1.4 Topic concerning the branch of medicine that deals with the infectious diseases of the tropics. Infectious tropical disease edamontology:topic_3414 1.4 Topic concerning the branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident. Trauma medicine edamontology:topic_3415 1.4 Topic concerning the branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents. Medical toxicology edamontology:topic_3416 1.4 Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine. Musculoskeletal disorders Musculoskeletal medicine edamontology:topic_3417 1.4 Topic concerning the branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles. Audiovestibular medicine Eye disoders Opthalmology edamontology:topic_3418 1.4 Topic concerning the branch of medicine that deals with the medical care of infants, children and adolescents. Child health Paediatrics edamontology:topic_3419 1.4 Mental health Topic concerning the branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour. Psychiatric disorders Psychiatry edamontology:topic_3420 1.4 Topic concerning the health of the reproductive processes, functions and systems at all stages of life. Audiovestibular medicine Family planning Fertility medicine Reproductive disorders Reproductive health edamontology:topic_3421 1.4 Topic concerning the use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance. Surgery edamontology:topic_3422 1.4 Topic concerning the branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney. Kidney disease Nephrology Urological disorders Urology Urology and nephrology edamontology:topic_3423 1.4 Alternative medicine Holistic medicine Topic concerning medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health. Complementary medicine edamontology:topic_3424 1.4 Topic concerning the skills used by a person to properly interact with others. In the business domain, the term generally refers to an employee's ability to get along with others while getting the job done. Interpersonal skills Business skills edamontology:topic_3425 1.4 Topic concerning the process of starting a business or other organisation. Entrepeneurship edamontology:topic_3426 1.4 Topic concerning the production, consumption and transfer of wealth. Economics edamontology:topic_3427 1.4 Topic concerning the process used to define a scientific study type and subtype, research question, hypotheses, independet and dependent variables, experimental design and, if applicable, data collection methods, statistical analysis plan and data management plan. Research study design edamontology:topic_3428 1.4 Topic concerning the impact of research on society. ELSI Ethical, legal and social implications edamontology:topic_3429 1.4 Topic concerning the process of creating clear and acurate documentation to describe research results, product use, and other medical information. Medical writing edamontology:topic_3430 1.4 Topic concerning process of writing scientic reports for publication in peer reviewed journals. Scientific writing edamontology:topic_3431 1.4 Topic concerning the process of creating any form of written technical communication including user manuals, technical manuals, help guides, standard operating procedures and work instructions. Technical writing edamontology:topic_3432 1.4 Topic concerning the ability to create and deliver engaging verbal presentations. Presentation skills edamontology:topic_3433 1.4 Topic concerning the application of processes, methods, knowledge, skills and experience to achieve project objectives on time and to budget. Project management edamontology:topic_3434 1.4 Topic concerning the use of English to communicate scientific concepts and results in a clear, unambiguous way appropriate to a scientific audience. Scientific English edamontology:topic_3435 1.4 Topic concerning the ability to train people to facilitate learning in others. Training for trainers edamontology:topic_3436 1.4 Topic concerning the activity of conveying information through the exchange of thoughts, messages or information as by speech, visuals, signals, writing or behaviour. Communication skills edamontology:topic_3437 1.4 Topic concerning the ability to organise or influence a group of people to achieve a common goal. Leadership skills edamontology:topic_3438 1.4 Topic concerning the objective analysis and evaluation of an issue in order to form a judgement. Critical thinking edamontology:topic_3439 1.4 Topic concerning support for or recommendation of a particular course of action, cause or policy. Advice and advocacy edamontology:topic_3440 1.4 Topic concerning the promotion and sale of products and services including market research and advertising. Marketing edamontology:topic_3441 1.4 Topic concerning the engagement of patients in research, development and policy. Patient advocacy Patient representation Patient engagement owl:Thing 19:06:2014 15:41 EDAM EDAM http://edamontology.org/ "EDAM relations and concept properties" EDAM_topic http://edamontology.org/topic_ "EDAM topics" Jon Ison application/rdf+xml BioMedical Topics : an ontology of biological and biomedical topics, created from merging the EDAM Topics sub-ontology with auxiliary topics that are out of scope of EDAM. 1.4 concept_properties "EDAM concept properties" relations "EDAM relations" topics "EDAM topics" Jon Ison