# Copyright 2002 PharmaDM N.V. # All rights reserved # # Special terms and conditions of use # # The information in this file can be freely used in the context of the # EU FP5 Quality of Life Project "BioMinT". All other use is reserved. # Use is subject to the conditions specified in the project's consortium # agreement on pre-existing know-how. In particular, any information in # this file will only be given to the project partners and to the extent # necessary for the project. This information can not be commercialised # without prior written agreement from PharmaDM. # PharmaDM makes no warranties, expressed or implied, with respect to data # contained in this file, and, furthermore, assumes no legal liability for # any party's use, or the results of such use, of any part of the data. # Semantics of this file # # Each line in this file represents one canonical form of a term representing # some (biological) influence. Fields are ";"-separated, and whitespace at # the beginning and end of each field is irrelevant. # # The first field on a line is the (canonical form of the) term itself. # # The second field is an indication of the place of the term in the # influence hierarchy, as follows : the top node of the hierarchy # has label E, and any term with label X.Y (with Y not containing # any ".") is a direct child node of the term with label X. Thus, # the node labels indicate a path from the top node to the term. # If a term occurs several times in this file with different labels, # this means there are multiple paths to this term. # (Actually, the shorter explanation is : this is the same syntax # as used in the MeSH.) # # The third field indicates the type of construct the term is typically # used in in relation to the other concepts of interest; 0-5 denote verb # constructs, e.g. 0 being the active subject-verb-location construct, # 6 and 7 are noun constructs, 8 and 9 are adjective constructs, and 10 # denotes "other" constructs. Here are typical examples of each # construct # 0 : A occurs in B # 1 : (no known examples) # 2 : B contains A # 3 : A is expressed in B # 4 : (X) finds A in B # 5 : A is found in B # 6 : ... the presence of A in B # 7 : (no known examples) # 8 : A is prevalent in B # 9 : B is rich in A # # The fourth field indicates if the term denotes a presence (0) or # an absence (1). # # Finally, the fifth field is a list of prepositions required for the # location (B in the above examples), if different from the # default for the construct. E.g. a protein A "occurs in" (or "at", # "on", etc.) a location B, but it is "absent _from_" B. # # For any more information or feedback, you can contact either # Kristof.VanBelleghem@pharmadm.com (especially concerning approach, # syntax and language constructs) or Andre.Vandecandelaere@pharmadm.com # (concerning biochemical content). #PRESENCE ONTOLOGY #TERM; NODE_LABEL; TYPE; MOOD; PREPOSITION_LIST CODE; TYPE; MOOD; PREPOSITION_LIST presence; E.0; 6; 0; present; E.0; 8; 0; occur; E.0; 0; 0; occurrence; E.0; 3; 0; # COMMENT:intrinsic presence absence; E.0.0; 6; 1; from absent; E.0.0; 8; 1; from prevail; E.0.1; 0; 0; prevalence; E.0.1; 6; 0; prevalent; E.0.1; 8; 0; # COMMENT: measured presence: characterized, detected, isolated from, identified, found, seen in, purified, deficient, lack, level, disribution in measure; E.0.1.0; 4; 0; measured; E.0.1.0; 5; 0; measurement; E.0.1.0; 6; 0; characterize; E.0.1.0.1; 4; 0; characterized; E.0.1.0.1; 5; 0; characterization; E.0.1.0.1; 6; 0; detect; E.0.1.0.2; 4; 0; detected; E.0.1.0.2; 5; 0; detection; E.0.1.0.2; 6; 0; isolate; E.0.1.0.3; 4; 0; from isolated; E.0.1.0.3; 5; 0; from isolation; E.0.1.0.3; 6; 0; from identify; E.0.1.0.4; 4; 0; identified; E.0.1.0.4; 5; 0; identification; E.0.1.0.4; 6; 0; find; E.0.1.0.5; 4; 0; found; E.0.1.0.5; 5; 0; see; E.0.1.0.6; 4; 0; seen; E.0.1.0.6; 5; 0; unseen; E.0.1.0.6; 8; 1; purify; E.0.1.0.7; 4; 0; from purified; E.0.1.0.7; 5; 0; from purification; E.0.1.0.7; 6; 0; from rich; E.0.1.0.8; 9; 0; in richness; E.0.1.0.8; 10; 0; deficient; E.0.1.0.8; 9; 1; in deficiency; E.0.1.0.8; 10; 1; #have; E.0.1.0.9; 2; 0; lack; E.0.1.0.10; 2; 1; lack; E.0.1.0.10; 6; 1; level; E.0.1.0.11; 6; 0; distribute; E.0.1.0.12; 4; 0; distributed; E.0.1.0.12; 5; 0; distribution; E.0.1.0.12; 6; 0; concentration; E.0.1.0.13; 6; 0; observe; E.0.1.0.14; 4; 0; observed; E.0.1.0.14; 5; 0; observation; E.0.1.0.14; 6; 0; # COMMENT: expressed presence: expressed in, overexpressing, developed, transcribe, synthesized in synthesize; E.0.1.1; 4; 0; synthesized; E.0.1.1; 5; 0; synthesis; E.0.1.1; 6; 0; express; E.0.1.1.0; 2; 0; expressed; E.0.1.1.0; 3; 0; by/in/on/at/within expression; E.0.1.1.0; 6; 0; by/in/on/at/within overexpress; E.0.1.1.1; 2; 0; overexpressed; E.0.1.1.1; 3; 0; by/in/on/at/within overexpression; E.0.1.1.1; 6; 0; by/in/on/at/within develop; E.0.1.1.2; 2; 0; developed; E.0.1.1.2; 3; 0; by/in/on/at/within development; E.0.1.1.2; 6; 0; by/in/on/at/within transcribe; E.0.1.1.3; 2; 0; transcribed; E.0.1.1.3; 3; 0; by/in/on/at/within transcription; E.0.1.1.3; 6; 0; by/in/on/at/within # COMMENT: changed presence: elevated, decreased, reappear, lost, reduplicate, depleted of, modified change; E.0.1.2; 4; 0; changed; E.0.1.2; 5; 0; change; E.0.1.2; 6; 0; elevate; E.0.1.2.0; 4; 0; elevated; E.0.1.2.0; 5; 0; elevation; E.0.1.2.0; 6; 0; decrease; E.0.1.2.1; 4; 0; decreased; E.0.1.2.1; 5; 0; decrease; E.0.1.2.1; 6; 0; reappear; E.0.1.2.2; 0; 0; reappearance; E.0.1.2.2; 6; 0; reduplicate; E.0.1.2.4; 4; 0; reduplicated; E.0.1.2.4; 5; 0; reduplication; E.0.1.2.4; 6; 0; deplete; E.0.1.2.5; 4; 0; depleted; E.0.1.2.5; 5; 0; from depletion; E.0.1.2.5; 6; 0; from # COMMENT: received presence: receive receive; E.0.2; 2; 0; received; E.0.2; 3; 0; by/in/on/at/within reception; E.0.2; 6; 0; by/in/on/at/within # COMMENT: induced presence: induced in, introduced in, cloned, down-regulated, transfected with, infected with induce; E.0.2.0; 4; 0; induced; E.0.2.0; 5; 0; induction; E.0.2.0; 6; 0; introduce; E.0.2.1; 4; 0; introduced; E.0.2.1; 5; 0; introduction; E.0.2.1; 6; 0; clone; E.0.2.2; 4; 0; cloned; E.0.2.2; 5; 0; cloning; E.0.2.2; 6; 0; down-regulate; E.0.2.3; 4; 0; down-regulated; E.0.2.3; 5; 0; down-regulation; E.0.2.3; 6; 0; infect; E.0.2.4; 10; 0; infected; E.0.2.4; 10; 0; infection; E.0.2.4; 6; 0; ; with; disinfect; E.0.2.5; 10; 1; disinfected; E.0.2.5; 10; 1; disinfection; E.0.2.5; 6; 1; transfect; E.0.2.6; 10; 0; transfected; E.0.2.6; 10; 0; transfection; E.0.2.6; 6; 0; # COMMENT: located presence (localization): located, localized, location, function at localize; E.0.3; 4; 0; localized; E.0.3; 5; 0; localization; E.0.3; 6; 0; locate; E.0.3.0; 4; 0; located; E.0.3.0; 5; 0; location; E.0.3.0; 6; 0; #function; E.0.3.1; 0; 0; at #function; E.0.3.1; 6; 0; at # COMMENT: correlated presence: to be bound to NEG to be dissociated from, retained, separated, colocalized associate; E.0.3.2; 4; 0; to/with associated; E.0.3.2; 5; 0; to/with association; E.0.3.2; 6; 0; to/with bind; E.0.3.2.0; 0; 0; to bound; E.0.3.2.0; 0; 0; to binding; E.0.3.2.0; 6; 0; to retain; E.0.3.2.1; 2; 0; retained; E.0.3.2.1; 3; 0; by/in/on/at/within retension; E.0.3.2.1; 6; 0; by/in/on/at/within colocalize; E.0.3.2.2; 4; 0; colocalized; E.0.3.2.2; 5; 0; colocalization; E.0.3.2.2; 6; 0; # COMMENT: motile presence (motion): relocate, circulates, move along|into, translocates from|to|along, transported from|to, cross move; E.0.3.3; 0; 0; in/along/into/onto/within/from/to motion; E.0.3.3; 6; 0; in/along/into/onto/within/from/to relocate; E.0.3.3.0; 0; 0; to relocate; E.0.3.3.0; 4; 0; to relocated; E.0.3.3.0; 5; 0; to relocation; E.0.3.3.0; 6; 0; to circulate; E.0.3.3.1; 0; 0; in/through circulation; E.0.3.3.1; 6; 0; in/through transport; E.0.3.3.2; 4; 0; in/from/to/along transported; E.0.3.3.2; 5; 0; in/from/to/along transport; E.0.3.3.2; 6; 0; in/from/to/along translocate; E.0.3.3.2.0; 4; 0; in/from/to/along translocated; E.0.3.3.2.0; 5; 0; in/from/to/along translocation; E.0.3.3.2.0; 6; 0; in/from/to/along dislocate; E.0.3.3.3; 4; 0; from dislocated; E.0.3.3.3; 5; 0; from dislocation; E.0.3.3.3; 6; 0; from cross; E.0.3.3.3; 0; 0; in/at/across/through crossing; E.0.3.3.3; 6; 0; in/at/across/through delocalize; E.0.4; 4; 0; delocalized; E.0.4; 5; 0; delocalization; E.0.4; 6; 0; locate; E.0.4.0; 4; 0; located; E.0.4.0; 5; 0; location; E.0.4.0; 6; 0; dissociate; E.0.4.2; 4; 0; from dissociated; E.0.4.2; 5; 0; from dissociation; E.0.4.2; 6; 0; from separate; E.0.4.2.0; 4; 0; from separated; E.0.4.2.0; 5; 0; from separation; E.0.4.2.0; 6; 0; from lose; E.0.4.2.1; 2; 0; lost; E.0.4.2.1; 3; 0; loss; E.0.4.2.1; 6; 0; by/in/on/at/within remove; E.0.4.2.2; 4; 0; from removed; E.0.4.2.2; 5; 0; from removal; E.0.4.2.2; 6; 0; from rest; E.0.4.3; 0; 0; rest; E.0.4.3; 6; 0; # COMMENT: stored presence: secreted, stored, released, harbor, enclosed, contain, content, available in store; E.0.5; 4; 0; stored; E.0.5; 5; 0; storage; E.0.5; 6; 0; secrete; E.0.5.0; 2; 0; secreted; E.0.5.0; 3; 0; by/from/in/on/at/within secretion; E.0.5.0; 6; 0; by/from/in/on/at/within absorb; E.0.5.1; 2; 0; absorbed; E.0.5.1; 3; 0; by/in/on/at/within absorption; E.0.5.1; 6; 0; by/in/on/at/within release; E.0.5.2; 2; 0; released; E.0.5.2; 3; 0; by/from/into/in/on/at/within release; E.0.5.2; 6; 0; by/from/into/in/on/at/within enclose; E.0.5.3; 2; 0; enclosed; E.0.5.3; 3; 0; enclosure; E.0.5.3; 6; 0; contain; E.0.5.4; 2; 0; contained; E.0.5.4; 3; 0; by/in/on/at/within content; E.0.5.4; 10; 0; harbor; E.0.5.4.0; 2; 0; harbored; E.0.5.4.0; 3; 0; available; E.0.5.5; 8; 0; source; E.0.5.6; 10; 0;