]> Functional activation of something by something else. activation Individuals of this type are the text of an article abstract article abstract A phenomenon or arrangement relating several biological entities. Examples include conjunctions and disjunctions of genes. In the text mining results, this merely means that the entities cooccur in some phrase. association A binding of something to something (e.g. of ligand to enzyme). binding An entity of biological interest such as a gene or an association among other biological entities; something that might be interpreted to be the thing meant by some piece of text. biological thing Expression of a gene. gene expression An individual of this type is either some particular gene or gene product (RNA, DNA, protein) concept, in the sense that a biologist would mean it, and as generally identifiable by, say, an Entrez Gene or Swissprot identifier. Barry Smith would probably say that these are really classes of molecules, not individuals. gene or gene product Functional inhibition of something by something else. inhibition A functional interaction among some things. interaction Functional localization of something by something else. localization A phrase from a particular abstract, identified by its content (as opposed to its position). phrase in context An individual of this type is putatively some functionally meaningful process involving biological things. For the Neurocommons text mining results, text is interpreted to be a process simply because there was an identified a subject, verb, and/or object. Other than this, a process is just another kind of association. process Functional regulation of something by something else. regulation A span (range) of text in a particular abstract, specified by position and length. span A selection of text from a particular source. text selection A count of the span's nontrivial associations. 'Nontrivial' means that different proteins/genes, or protein/gene-containing associations, are somehow related to one another. This is used by the Neurocommons developers in statistics gathering. association count Relates a record to its primary key (for example: a PubMed record to a PubMed id). has id A count of the span's nontrivial interactions, considering only the ones that have an identified process verb (activation, etc.). This is used by the Neurocommons developers in statistics gathering. interaction count Relates a span of text to its length, in characters. Whether this means octets, Unicode codepoints, or something else has yet to be determined. has length Relates a phrase-in-context to its text (as a string). has phrase Relates an Entrez record to the name of a 'chunk' of a PubMed distribution, e.g. 'medline07n0498'. This is for use by the Neurocommons developers for debugging. is in chunk Relates a span of text to its starting position in its containing text (e.g. the position of a span in an abstract). starts at Relates a publication record to the abstract of the article it describes. has abstract Relates a phrase to a larger context in which it occurs (e.g. an article abstract). has context has participant P has-effector X means that X is considered functionally responsible for the process P. has effector Relates some text to a biological interpretation of that text. has interpretation Relates a textual phrase to a gene-or-gene-product concept that it putatively identifies. The identification assumes that the phrase describes a human gene or protein; if the phrase is meant to identify a non-human gene, then all bets are off. identifies Relates some text to a biological interpretation of that text, according to the results of a text mining process designated as 'Neurocommons 0.0'. has nc0.0 interpretation P has-object Y means that Y is considered to be acted upon by something in process P. has as its object or target Relates something to a 'smaller' phenomenon that helps to define it. E.g. a protein participates in a process that involves it; or a gene participates in an association denoting the conjunction of that gene with several others. has participant Relates a gene-or-gene-product to a gene record that might describe it. is described by Relates a gene-or-gene-product to a protein record that might describe it. is described by