KGES_CuratedTermList

	A	C	D	E	F	G	H	J	L	M	N	O	P	Q	R	S	T	U	V	W	X	Z	AA	AC	AD
1		Labels				Synonyms					Source Details						Annotations / Notes
2	Concept	Context	Preferred Label	Alternate Label	Abbreviation	Synonym	Synonym Context	Identifier	Definition (text)		Concept Source	Preferred Label Source	Alternate Label Source	Definition Source (isDefinedBy)	Definition Adapted from Source		Scope Note	Explanatory Note	Usage Note	Example	Dependencies	Parent Concept	Equivalent Concept	Concept/Definition Usage (Literature)	References

3	Object Type	Passages, Sentences, Annotation files, Clauses, Entity Mentions, Event Mentions, Entities, Epistemics, Links, Contexts, Example context, Absolute Text Positions (or Offsets), Relative Contextualized Text Positions, Map Representation, NEW Phosphorylation at site, NEW translocation, OLD entity mentions and relations	Object Type	object-type				object-type	Each extracted entity has a object-type		FRIES-output-spec-v0.10_160502.txt	FRIES		https://docs.oracle.com/cd/B28359_01/appdev.111/b28425/obj_types.htm						"frame-collection"
4	Object Metadata	Annotation files, Passages, Sentences, Clauses, Entity Mentions, Event Mentions, Entities, Epistemics, Links, Contexts, Map Representation, NEW Phosphorylation at site, NEW translocation, OLD entity mentions and relations,	Object Metadata	object-meta				object-meta	Meta data associated with											{"object-type": "meta-info", "component": "nxml2fries"}
5	Frames	Annotation files, Links	Frames	frames				frames
6	Frame	Passages, Sentences, Clauses, Entity Mentions, Event Mentions, Entities, Epistemics, Links, Contexts, Example context, Map Representation	Frame	frame				frame	An information unit or tuple containing the meta information of an extracted mention	*										{ "object-type": "frame", "object-meta": {"object-type": "meta-info", "component": "nxml2fries"}, "frame-id": "pass-PMC3847091-uaz-r13-11", "frame-type": "passage", "index": 11, "section-id": "s1", "section-name": null, "is-title": false, "text": "..." }
7	Frame ID	Passages	Frame ID	frame-id				frame-id												"pass-PMC3847091-uaz-r13-11"
8	Frame Collection		Frame Collection	frame-collection				frame-collection	A collection of frames	*										"entity-mention"
9	Frame Type	Passages	Frame Type	frame-type				frame-type												"passage"
10	Passage	Passages	Passage	passage				passage												"pass-PMC3847091-uaz-r13-11"
11	Index	Passages	Index	index				index												10
12	Section ID	Passages	Section ID	section-id				section-id												"s1"
13	Section Name	Passages	Section Name	section-name				section-name
14	Is Title?	Passages	Is Title?	is-title				is-title												FALSE
15	Text	Passages, Sentences, Clauses, Entity Mentions, Event Mentions	Text	text				text	Any free or plain text, typically for human consumption and in English. Can instantiate also as a textual search query.					http://edamontology.org/data_3671						"Consequently, the pro-apoptotic activity of ASPP2 is increased by the RAS/Raf/MAPK signalling cascade as ASPP2 phosphorylation mutant fails to do so."
16	Organization	Annotation files, Entities, Epistemics, Links, Contexts	Organization	organization		Org		organization	An organization is a collective with a complex articulation of tasks, roles and responsibilities					SIO_000012						"CMU"
17	Document ID	Annotation files	Document ID	doc-id				doc-id												"PMC3847091"
18	Processing Start		Processing Start	processing-start				processing-start												"2015-05-13 04:58:48"
19	Processing End		Processing End	processing-end				processing-end												"2015-05-13 04:59:30"
20	Metadata Information		Metadata Information	meta-info				meta-info
21	Entity Mention		Entity Mention	entity-mention				entity-mention	occurance frame of a named entity found in a text passage					https://en.wikipedia.org/wiki/Entity_linking
22	Clause		Clause	clause				clause	A clause consists of a subject and a predicate.					SIO:000493
23	Sentence		Sentence	sentence				sentence	A sentence is a grammatical unit consisting of one or more words that bear minimal syntactic relation to the words that precede or follow it.					SIO_000113						"sent-PMC3847091-uaz-r1-0-0"
24	Component		Component	component				component	Cross reference pointing to a Gene Ontology -'cellular component' term.					MI:0354						"REACH"
25	Type		Type	type				type												"protein"
26	Subtype		Subtype	subtype				subtype												"phosphorylation"
27	Arguments		Arguments	arguments				arguments
28	Argument		Argument	argument		Arg		argument	An argument is a set of one or more declarative sentences (or propositions) known as the premises along with another declarative sentence (or proposition) known as the conclusion.					SIO:000259
29	Is Negated?		Is Negated?	is-negated				is-negated												TRUE
30	Relation Mention		Relation Mention	relation-mention				relation-mention
31	Members		Members	members				members												["ment-PMC3902907-cmu-junsys-r1-98-1", ...]
32	Value		Value	value				value												0.6
33	Status		Status	status				status	An attribute describing the status of a feature, based on the available evidence.					SO:0000905						"hypothesis"
34	Hypothesis		Hypothesis	hypothesis				hypothesis	A hypothesis is a proposed explanation for a phenomenon.					SIO_000284
35	Specialization Of		Specialization Of	specialization-of				specialization-of	is specialization of is a relation between a more specific instance (in terms of spatial/temporal localization & other attributres) than the other.					SIO:001096
36	Score		Score	score				score	A numerical value, that is some type of scored value arising for example from a prediction method.					http://edamontology.org/data_1772						0.9
37	Context		Context	context				context												"that activated the tyrosine kinase Janus kinase"
38	Epistemics		Epistemics	epistemics				epistemics
39	Entity		Entity	entity				entity	Every thing is an entity.					SIO_000000
40	Scope		Scope	scope				scope												"sent-PMC3847091-uaz-r13-11-2"
41	Cell Line	Entity Mention Type	Cell Line	cell-line				cell-line	A cell line is a collection of genetically identifical cells.					SIO_010054						[ "cellosaurus:DG-75" ]
42	Cell Type	Entity Mention Type	Cell Type	cell-type				cell-type	A cell type is a distinct morphological or functional form of cell. Examples are epithelial, glial etc.					EFO_0000324						["type name or database:identifier pair", ...]
43	Tissue Type	Entity Mention Type	Tissue Type	tissue-type				tissue-type												["type name or database:identifier pair", ...]
44	Location		Location	location				location	A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.					PATO:0000140						[ "go:GO:0044299", "go:GO:0005794" ]
45	Organism		Organism	organism				organism	A biological organisn is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not).					SIO_010000						[ "taxonomy:10090", "taxonomy:9606" ]
46	Organ	Entity Mention Type	Organ	organ				organ	Anatomical structure that performs a specific function or group of functions [WP].	*				UBERON:0000062						["name or database:identifier pair" ...]
47	Offset		Offset	offset				offset	A positional quality inhering in a bearer by virtue of the bearer's position being displaced from a reference point.					PATO:0002436						380
48	Absolute Position		Absolute Position	absolute-pos				absolute-pos
49	Relative Position		Relative Position	relative-pos				relative-pos
50	Reference		Reference	reference				reference	A reference is a textual entity that describes a single source used in the preparation or development of the work.					SIO_000176						"sent-PMC3847091-uaz-r13-11-2"
51	Context Start		Context Start	context-start				context-start												"ASPP2/2"
52	Context End		Context End	context-end				context-end												"ASPP2/2"
53	Is Closed?		Is Closed?	is-closed				is-closed												FALSE
54	Map		Map	map				map	A map is a a visual representation of an area that depicts the relationship between elements of that space.					SIO:000906						[{"object-type": "mapping", "from": "sent-PMC3847091-uaz-r13-1-1", "to": "sent-PMC3847091-cmu-r4-1"}, {"object-type": "mapping", "from": "sent-PMC3847091-uaz-r13-1-2", "to": "sent-PMC3847091-cmu-r4-2"}, {"object-type: "mapping", "from": "sent-PMC3847091-uaz-r13-1-3", "to": "sent-PMC3847091-cmu-r4-3", "s1": 10, "e1": 100}, {"object-type: "mapping", "from": "sent-PMC3847091-uaz-r13-1-4", "to": "sent-PMC3847091-cmu-r4-4", "s2": 15, "e2": 95}, {"object-type: "mapping", "from": "sent-PMC3847091-uaz-r13-1-5", "to": "sent-PMC3847091-cmu-r4-6", "s1": 5, "e1": 50, "s2": 20, "e2": 68}, .....]
55	Mapping		Mapping	mapping				mapping	Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts.					http://www.ontobee.org/ontology/EDAM?iri=http://edamontology.org/operation_2429
56	From		From	from				from												"sent-PMC3847091-uaz-r13-1-4"
57	To		To	to				to												"sent-PMC3847091-cmu-r4-2"
58	Submitter		Submitter	submitter				submitter	A study personnel role played by a party who reports the outcome of a study component					http://purl.obolibrary.org/obo/OBI_0000068						"UAZ"
59	Namespace		Namespace	namespace				namespace	A namespace is an informational entity that defines a logical container for a set of symbols or identifiers.					SIO:000067						"uniprotkb"
60	Polarity		Polarity	polarity				polarity	A molecular quality that inheres in a molecular entity by virtue of whether or not the molecular entity has a separation of electric charge which leads to the molecule having an electric dipole.					PATO_0002186						"positive"
61	start position		Start Position	start-pos				start-pos	A start position is the proximal position of an object relative to an origin in a linear system.					SIO_000943						{"object-type": "relative-pos", "reference": "pass-PMC3847091-uaz-r13-11", "offset": 194}
62	End Position		End Position	end-pos				end-pos	An end position is the distal position of an object relative to an origin in a linear system.					SIO_000953						{"object-type": "relative-pos", "reference": "pass-PMC3847091-uaz-r13-11", "offset": 343, "is-closed": false}
63	Inconsistency		Inconsistency	inconsistency				inconsistency	The term used to define the general concept where an issue is detected in the generated knowledge graph.
64	Entity Label Misclassification		Entity Label Misclassification	entity-label-misclassification				entity-label-misclassification	General class of inconsistency that is defined by an extraction mismatch to the entity mention labels.
65	Mismatch Entity Label Inconsistency	If two entity mentions with the same label and the same context, such as P200 fromSentence sent-1, have different mention types that are disjoint from each other, then is mismatch entity label inconsistency occurs	Mismatch Entity Label Inconsistency	mismatch-entity-label-inconsistency				mismatch-entity-label-inconsistency	General class of inconsistency for occurrences of the same entity with different labels
66	Boundary Label Mapping Inconsistency	If two entity mentions have the same type but the boundaries have different relative start and end positions, it is a Boundary label mapping inconsistency	Boundary Label Mapping Inconsistency	boundary-label-mapping-inconsistency				boundary-label-mapping-inconsistency	Schema label mismatch of partial extracted label
67	Disjointness Inconsistency	If two mentions have the same label and context but are assigned to types asserted as disjoint in the ontology, there is a disjointness inconsistency	Disjointness Inconsistency	disjointness-inconsistency				disjointness-inconsistency	General class of inconsistency that is defined by an individual has an incorrect relation with another individual. This can pertain in regards to general hierarchy or properties.
68	Entity Disjointess	This is a subclass of the disjointness inconsistency where the mentions involved are entity mentions	Entity Disjointess	entity-disjointess				entity-disjointess	Disjointness inconsistency where the extracted entities have an incorresponding types with one another.
69	Event Disjointess	This is a subclass of the disjointness inconsistency where the mentions involved are event mentions	Event Disjointess	event-disjointess				event	Disjointness inconsistency where the extracted events have an incorrect relationship to one another.
70	Rule		Rule	rule				rule	A rule is an executable which guides, defines, or restricts actions					OBI_0500021
71	Relation Disjointess	In relation disjointness, we look for the same set of extracted trigger entities and make sure that their extracted relationships do not include those that are asserted to be disjoint.	Relation Disjointess	relation-disjointess				relation	Disjointness inconsistency where the predicate connection shared between the extracted entities is incorrect.
72	Event Mention		Event Mention	event-mention				event-mention	occurance frame of a named event found in a text passage
73	Percentage		Percentage	percentage				percentage	a proportion of something expressed as a percentage amount
74	Restricted Percentage		Restricted Percentage	restricted-percentage				restricted-percentage	a proportion of something expressed as a percentage amount and not exceeding 100% of that of which it is the percentage
75	Mention Type		Class Type	class-type				mention-type	Superclass of entity and event types	*
76	Entity Mention Type		Entity Mention Type	entity-mention-type				entity-mention-type	Superclass of entity types that are recognized by the IE Extraction System.	*
77	Bioprocess	Entity Mention Type	Bioprocess	bioprocess				bioprocess	A specific process that uses complete living cells or their components (e.g., bacteria, enzymes, chloroplasts) to obtain desired products.	*				https://en.wikipedia.org/wiki/Bioprocess		*
78	Cellular Component	Entity Mention Type	Cellular Component	cellular-component				cellular-component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.	*				http://purl.obolibrary.org/obo/GO_0005575		*
79	Family	Entity Mention Type	Family	family				family	One of the eight major taxonomic ranks of biological classification, which is classified between order and genus, and may be divided into subfamilies, which are intermediate ranks above the rank of genus.	*				https://en.wikipedia.org/wiki/Family_(biology)		*
80	Gene-or-Gene Product	Entity Mention Type	Gene-or-Gene Product	gene-or-gene-product				gene-or-gene-product	The biochemical material, either RNA or protein, resulting from expression of a gene. A measurement of the amount of gene product is sometimes used to infer how active a gene is.	*				https://en.wikipedia.org/wiki/Gene_product		*
81	Protein	Entity Mention Type	Protein	protein				protein	An organic polymer that is composed of one or more linear polymers of amino acids.	*				SIO:010043		*
82	Simple-Chemical	Entity Mention Type	Simple-Chemical	simple-chemical				simple-chemical
83	Site	Entity Mention Type	Site	site				site	The specific region of an enzyme where a substrate binds and catalysis takes place or where chemical reaction occurs.	*				http://www.biology-online.org/dictionary/Active_site		*
84	Species	Entity Mention Type	Species	species				species	An individual belonging to a group of organisms (or the entire group itself) having common characteristics and (usually) are capable of mating with one another to produce fertile offspring.	*				http://www.biology-online.org/dictionary/Species		*
85	Event Mention Subtype		Event Mention Subtype	event-mention-subtype				event-mention-subtype	Superclass of event subtypes that are recognized by the IE Extraction System.	*
86	Acetylation	Event Mention Subtype	Acetylation	acetylation				acetylation	The addition of an acetyl group to a protein amino acid.	*				GO_0006473		*
87	Autophosphorylation	Event Mention Subtype	Autophosphorylation	autophosphorylation				autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).	*				GO_0046777		*
88	Deacetylation	Event Mention Subtype	Deacetylation	deacetylation				deacetylation	The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.	*				GO_0006476
89	Deglycosylation	Event Mention Subtype	Deglycosylation	deglycosylation				deglycosylation	The removal of sugar residues from a glycosylated protein.	*				GO_0006517
90	Demethylation	Event Mention Subtype	Demethylation	demethylation				demethylation	The process of removing one or more methyl groups from a molecule.	*				GO_0070988
91	Dephosphorylation	Event Mention Subtype	Dephosphorylation	dephosphorylation				dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.	*				GO_0016311
92	Farnesylation	Event Mention Subtype	Farnesylation	farnesylation				farnesylation	The covalent attachment of a farnesyl group to a protein.	*				GO_0018343
93	Glycosylation	Event Mention Subtype	Glycosylation	glycosylation				glycosylation	The covalent attachment and further modification of carbohydrate residues to a substrate molecule.	*				GO_0070085
94	Hydrolysis	Event Mention Subtype	Hydrolysis	hydrolysis				hydrolysis	A solvolysis reaction where the solvent material is water.	*				MOP_0000619
95	Hydroxylation	Event Mention Subtype	Hydroxylation	hydroxylation				hydroxylation	The addition of a hydroxy group to a protein amino acid.	*				GO_0018126
96	Methylation	Event Mention Subtype	Methylation	methylation				methylation	The process in which a methyl group is covalently attached to a molecule.	*				GO_0032259
97	Phosphorylation	Event Mention Subtype	Phosphorylation	phosphorylation				phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.	*				GO_0016310
98	Ribosylation	Event Mention Subtype	Ribosylation	ribosylation				ribosylation	The transfer, from NAD, of ADP-ribose to protein amino acids.	*				GO_0006471
99	Sumoylation	Event Mention Subtype	Sumoylation	sumoylation				sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.	*				GO_0016925
100	Translocation	Event Mention Subtype	Translocation	translocation				translocation	The directed movement of a molecule(s) produced by an organism to a location inside a second organism, where the two organisms are in a symbiotic interaction	*				GO_0051836