BISON - Concept Definition

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Contents 1 BISON_vacabulary 1.1 BISON_objects 1.1.1 singleton_object 1.1.1.1 sequence 1.1.1.1.1 protein_sequence 1.1.1.1.2 nucleic_acid_sequence 1.1.1.2 microarray 1.1.1.3 structure 1.1.1.3.1 protein_structure 1.1.1.4 SNP 1.1.1.5 phenotype 1.1.1.6 id 1.1.2 set_objects 1.1.2.1 sequence_set 1.1.2.1.1 protein_sequence_set 1.1.2.1.2 gene_sequence_set 1.1.2.2 microarray_set 1.1.2.3 protein_structure_set 1.1.2.4 alignment 1.1.2.4.1 sequence_alignment 1.1.2.4.2 structure_alignment 1.1.2.5 gene_set 1.1.2.6 SNP_set 1.1.2.7 phenotype_set 1.1.2.8 id_set 1.1.3 complex_object 1.1.3.1 pattern 1.1.3.1.1 sequence_motif 1.1.3.1.2 structural_domain 1.1.3.2 =clustering_pattern 1.1.3.2.1 network_module 1.1.3.3 interactions 1.1.3.3.1 regulatory_network 1.1.3.4 network 1.1.3.4.1 regulatory_network 1.1.3.4.2 network_module 1.1.3.4.3 metabolic_pathway 1.1.3.5 annotation_file 1.1.3.6 ontology 1.2 matrix 1.2.1 adjacency_matrix 1.2.2 microarray_set 1.3 set 1.3.1 gene_set 1.4 ontology 1.5 macromolecule 1.5.1 polysaccharides 1.5.2 nucleic_acids 1.5.3 chromosome 1.5.4 protein 1.6 disease 1.7 Pvalued

BISON_vacabulary

BISON_vacabulary is the parent of all concepts. It includes all conceptal biological concepts as well as concrete concepts that are used in data analysis. For example, an alllele is a conceptual concept, while sequence is a concrete concept.

BISON_objects

Concept BISON_objects represent all biological concepts that are used in data analysis. For example, sequence and gene_expression are two concepts wildly used in data analysis.

singleton_object

Concept singleton_object represents a single unit biological object. For example, sequence and SNP.

sequence

Concept sequence is defined as the order in which subunits appear in a chain, such as amino acids in a polypeptide or nucleotide bases in a dNA or rNA molecule. Here it represents the string of characters, which can either be amino acids or nucleotides.

protein_sequence

Concept protein_sequence represent the string of amino acids and has properties associated with proteins. For example, protein will contain motifs, be enzymatic or not and so on.

nucleic_acid_sequence

Concept nucleic_acid_sequence is a string of nucleotides.

microarray

Concept microarray represents the expressions of a given gene set under a specific condition.

structure

Concept structure represents both nucleic acid and protein structures.

protein_structure

Concept protein_structure represents PDB format protein structure.

SNP

Concept SNP represents a DNA sequence variation occurring when a single nucleotide - A, T, C, or G - in the genome (or other shared sequence) differs between members of a species (or between paired chromosomes in an individual). (From http://en.wikipedia.org)

phenotype

Concept phenotype here only represents a specific manifestation of a trait that varies between individuals. (From http://en.wikipedia.org/).

id

Concept id represents all ids.

set_objects

Concept id represents all ids.

sequence_set

Concept sequence_set represents set of sequences.

protein_sequence_set

gene_sequence_set

microarray_set

Concept microarray_set represents the collections of microarrays.

protein_structure_set

Concept protein_structure_set represents a set of PDB format protein structures.

alignment

Concept alignment represents all alignments, such as sequence alignment and protein structure alignment.

sequence_alignment

Concept sequence_alignment represents gene and protein sequence alignments.

structure_alignment

Concept structure_alignment represents protein structure alignment.

gene_set

Concept gene_set represents the collection of genes. It can be a set of gene ids or a set of gene sequences.

SNP_set

Concept SNP_set represents a set of SNPs.

phenotype_set

Concept phenotype_set represents the collection of a set of phenotypes.

id_set

Concept id_set represents a set of ids.

complex_object

Concept complex_object represents concepts that requires the combination of multiple simple concepts and their relationships. For example, concept pattern requires an object that contains the pattern as well as the pattern itself.

pattern

Concept pattern represents the patterns in sequence, protein structure, network and clustering result.

sequence_motif

Concept sequence_motif is defined as a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. (From http://en.wikipedia.org)

structural_domain

Concept structural_domain is defined as an element of overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. (From http://en.wikipedia.org/)

=clustering_pattern

Concept clustering_pattern represents the clusters from a clustering alogorithm.

network_module

Concept network_module is a subset of network which has a pattern associated.

interactions

Concept interactions represents all the interactions in cell, such as protein-protein interaction, protein-DNA interaction and so on.

regulatory_network

Concept regulatory_network represents the actions between transcripion factors and target genes.

network

Concept network represents all network related concepts, such as regulatory network, metabolic network and so on.

regulatory_network

Concept regulatory_network represents the actions between transcripion factors and target genes.

network_module

Concept network_module is a subset of network which has a pattern associated.

metabolic_pathway

Concept metabolic_pathway represents the metabolic pathway and the reactions in the pathway.

annotation_file

Concept annotation_file represents all annoted files, such as gene annotation, protein structure annotation and so on.

ontology

Concept ontology represents all the ontologies that are used in biological and medical fields.

matrix

Concept matrix represents all matrix format data.

adjacency_matrix

microarray_set

Concept microarray_set represents the collections of microarrays.

set

Concept set represents all conceptual set concepts.

gene_set

Concept gene_set represents the collection of genes. It can be a set of gene ids or a set of gene sequences.

ontology

Concept ontology represents all the ontologies that are used in biological and medical fields.

macromolecule

Concept macromolecule is defined as a large molecule with a large molecular mass bonded covalently.

polysaccharides

Concept polysaccharides is defined as polymers made up of many monosaccharides joined together by glycosidic linkages. (From http://en.wikipedia.org)

nucleic_acids

Concept nucleic_acids is defined as a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. (From http://en.wikipedia.org/)

chromosome

A chromosome is a single large macromolecule of DNA, and constitutes a physically organized form of DNA in a cell. It is a very long, continuous piece of DNA (a single DNA molecule), which contains many genes, regulatory elements and other intervening nucleotide sequences. (From http://http://en.wikipedia.org).

protein

Concept protein here is defined as relatively large organic compounds made of amino acids arranged in a linear chain and joined together between the carboxyl atom of one amino acid and the amine nitrogen of another. (From http://en.wikipedia.org/)

disease

Concept disease represents the UMLS code of diseases and can be associated with chromosomes and genes.

Pvalued

Concept Pvalued represented the score of comparions.