UMLS语义网络

1、UMUMUMLS? Refere nee ManuaUMLS° Reference ManualU.S. National Library of Medicine5: Sema ntic NetworkThe Sema ntic Network con sists of (1) a set of broad subject categories, or Sema ntic Types, that provide a con siste nt categorizati on of all con cepts represe nted in the UMLS Metathesaurus,

2、 and (2) a set of useful and importa nt relati on ships, or Sema ntic Relati ons, that exist betwee n Sema ntic Types. This sect ion of the docume ntati on provides an overview of the Sema ntic Network, and describes the files of the Sema ntic Network. Sample records illustrate structure and content

3、 of these files.LS? Refere nee Man ualThe Semantic Network is distributed as one of the UMLS Knowledge Sources and as an open source resource available on the Sema ntic Network Web site, subject to these terms and con diti ons.5.1 OverviewThe purpose of the Sema ntic Network is to provide a con sist

4、e nt categorizati on of all con cepts represe nted in the UMLS Metathesaurus and to provide a set of useful relati on ships betwee n these con cepts. All in formatio n about specific con cepts is found in the Metathesaurus. The Network provides in formatio n about the set of basic sema ntic types, o

5、r categories, which may be assig ned to these con cepts, and it defi nes the set of relati on ships that may hold betwee n the sema ntic types. The Sema ntic Network contains 133 sema ntic types and 54 relati on ships. The Sema ntic Network serves as an authority for the sema ntic types that are ass

6、ig ned to con cepts in the Metathesaurus. The Network defi nes these types, both with textual descripti ons and by means of the in formati on in here nt in its hierarchies.The sema ntic types are the no des in the Network, and the relati on ships betwee n them are the in ks. There are major group in

7、gs of sema ntic types for orga ni sms, an atomical structures, )iologic fun cti on, chemicals, eve nts, physical objects, and con cepts or ideas. The curre nt scope of the UMLS semantic types is quite broad, allowing for the semantic categorization of a wide range of term ino logy in multiple doma i

8、ns.The Metathesaurus con sists of terms from its source vocabularies. The meaning of each term is defi ned by its source, explicitly by defi niti on or anno tati on; by con text (its place in a hierarchy); by synonyms and other stated relati on ships betwee n terms; and by its usage in description,

9、classification, or indexing. Each Metathesaurus concept is assigned at least one sema ntic type. In all cases, the most specific sema ntic type available in the hierarchy is assig ned to the con cept. For example, the con cept "Macaca" receives the sema ntic type "Mammal" because

10、 there is not a more specific type "Primate" available in the Network. The level of gra nu larity varies across the Network. This has importa nt implicati ons for in terpret ing the meaning (i.e., sema ntic type) that has bee n assig ned to a Metathesaurus con cept. For example, a sub-tree

11、 un der the node "Physical Object" is "Ma nu factured Object". It has only two child no des, "Medical Device" and "Research Device". It is clear that there are manu factured objects other tha n medical devices and research devices. Rather tha n proliferate the

12、 nu mber of sema ntic types to en compass multiple additi onal subcategories for these objects, con cepts that are n either medical devices nor research devices are simply assig ned the more gen eral sema ntic typeLS? Refere nee Man uaMa nufactured Object".Figure 1 illustrates a porti on of the

13、 Network. The sema ntic type "Biologic Fun cti on" has two childre n, "Physiologic Function" and "Pathologic Fun cti on", and each of these in turn has several childre n and gran dchildre n. Each child in the hierarchy is lin ked to its pare nt by the "isa" li

14、 nk.Page 4The primary link in the Network is the "isa" link. This establishes the hierarchy of types within the Network and is used for decidi ng on the most specific sema ntic type available for assig nment to a Metathesaurus con cept. I n additi on, a set of non-hierarchical relati ons b

15、etwee n the types has been identified. These are grouped into five major categories, which are themselves relati on s: "physically related to", "spatially related to", "temporally related to", "function ally related to", and "con ceptually related to"

16、;.Figure 2 illustrates a porti on of the hierarchy for Network relati on ships. The "affects" relatio nship, one of several fun cti onal relati on ships, has six childre n, in cludi ng "ma nages", "treats", and "preve nts".The relatio ns are stated betwee n hi

17、gh level sema ntic types in the Network whe never possible and are gen erally in herited via the "isa" li nk by all the childre n of those types. Thus, forexample, the relati on "process of" is stated to hold betwee n the sema ntic types "BiologicUMLS? Refere nee Manu aFu nc

18、tio n" and "Orga ni sm". Therefore, it also holds between "Orga n or Tissue Fun ctio n" (whichis a "Physiologic Function", which is, i n turn, a "Biologic Function") and "An imal" (which isan "Orga ni sm"). The relati ons are stated be

19、twee n sema ntic types and do not n ecessarily apply to all in sta nces of con cepts that have bee n assig ned to those sema ntic types. That is, the relatio n may or may not hold betwee n any particular pair of con cepts. So, though the relati on"evaluati on of" holds betwee n the sema nt

20、ic types "Sig n" and "Orga nism Attribute", a particular sig n or a particular attribute may not be lin ked by this relati on. Thus, sig ns such as "overweight" and "fever" are evaluations of the organism attributes "body weight" and "body tempe

21、rature", respectively. However, "overweight" is not an evaluation of "body temperature", and "fever"is not an evaluation of "body weight".In some cases there will be a con flict betwee n the placeme nt of types in the Network and the link to be inherited.

22、 If so, the inheritance of the link is said to be blocked. For example, by in herita nce, the type "Me ntal Process" would be "process of" "Pla nt". Since pla nts are not sen tie nt bein gs, this link is explicitly blocked. In other cases the n ature of the relati on is

23、 such that it should not be inherited by the children of the types that it links. In that case, the relation is defined for the two semantic types it explicitly links, but blocked for all the children of those types. For example, "con ceptual part of" li nks "Body System" and &qu

24、ot;Fully Formed An atomicalUMLS? Refere nce Manu aStructure", but it should n ot li nk "Body System" to all the childre n of "Fully Formed An atomical Structure", such as "Cell" or "Tissue".Several porti ons of the MeSH hierarchy have bee n labeled with c

25、hild to pare nt sema ntic relatio nships. All of the an atomy, diseases, and psychiatry and psychology sect ions have bee n labeled, as well as a porti on of the biological scie nces sect ion. The links that are expressed betwee n MeSH terms are, with a few excepti ons, reflected in the Sema ntic Ne

26、twork. That is, if two MeSH terms are linked by a certain relation, then that link is expressed in the Network as a link betwee n the sema ntic types that have bee n assig ned to those MeSH terms. For example, "Amniotic Fluid", which is a "Body Substance", is a child of "Emb

27、ryo", which is an "Embryonic Structure". The labeled relati on ship betwee n "Amn iotic Fluid" and its pare nt "Embryo" is "surroun ds". This is allowable, since the relati on "Body Substa nce surro unds Embry onic Structure" is represe nted in

28、the Network.Figure 3 shows a portion of the Semantic Network, illustrating the relations, either hierarchical or associative, that exist betwee n sema ntic types.The UMLS Semantic Network is provided in two formats: a relational table format and a unit UMLS? Refere nce Man uaecord format.5.2 Sema nt

29、ic Network ASCII Relatio nal FormatThere are two basic tables, two ancillary tables, and two bookkeeping tables included in this format. The two basic tables con tain exactly the same in formatio n as the un it record file, but the in formati on is prese nted differe ntly. One table contains defi ni

30、ti onal in formatio n about the sema ntic types and relati ons; the other contains in formatio n about the structure of the Network. Each semantic type and each relation has been assigned a four character unique identifier (Ul). These are of the form "T001", "T002", etc. The an c

31、illary tables are expa nsions of the table that contains the Network structure. They give the fully in herited set of links represe nted in the Network. The first table is expressed as triples of UI's. The sec ond is expressed as triples of names. The two bookkeeping tables describe the relation

32、al files and their fields. Fields in all tables are separated by a "|". All tables are listed and described below:UMLS?©aerenceDManunalSRDEFBasic information about the Semantic Types and Relations.SRSTRStructure of the Network.SRSTRE1Fully inherited set of Relations (UI's).SRSTRE2

33、Fully inherited set of Relations (names).SRFILDescription of each table.SRFLDDescription of each field and the table(s) in which it is found.Specific Descriptions of each Table:UMLS?FieldDescriptionRT:Record Type (STY = Semantic Type or RL = Relation).Ul:Unique Identifier of the Semantic Type or Rel

34、ation.J MkanutSd Semantic Type or Relation.STN/RTN:Tree Number of the Semantic Type or Relation.DEF:Definition of the Semantic Type or Relation.EX:Examples of Metathesaurus concepts with this Semantic Type (STY records only).UN:Usage note for Semantic Type assignment (STY records only).NH:The Semant

35、ic Type and its descendants allow the non-human flag (STY records only).ABR:Abbreviation of the Relation Name or Semantic Type.RIN:Inverse of the Relation (RL records only).Table: SRDEFSemantic NetworkPage #Semantic NetworkPage #Table: SRSTRUMLS?FieldDescriptionSTY/RL:Argument 1 (Name of a Semantic

36、Type or Relation).RL:Relation ("isa" or the name of a non-hierarchical Relation).ferbnc'世rgManuOName of a Semantic Type or Relation); if this field is blank this means that the Semantic Type or Relation is one of the top noSesof'theNetwork.Semantic NetworkPage 5Semantic NetworkPage

37、 #LS:Link Status (D = Defined for the Arguments and its children; B = Blocked; DNI = Defined but Not Inherited by the children of the Arguments).N.B.: The relations expressed in this table are binary relations and the arguments are ordered pairs. The relations are stated only for the top-most node o

38、f the "isa" hierarchy of the Semantic Types to which they may apply.Table: SRSTRE1 or SRSTRE2UMLS?FieldDescriptionUI/STY:Argument 1 (UI or name of a Semantic Type).UI/RL:Relation (UI or name of a nonhierarchical Relation).UI/STY:、eferen(Argument 2 (UI or name of a Semantic Type).N.B.: The

39、relations expressed in this table are binary relations and the arguments are ordered pairs. All relations have been fully inherited :eManualSemantic NetworkPage #Semantic NetworkPage 9Table: SRFILFieldDescriptionFIL:File Name.DES:Description of the file.FMT:Format of the file (fields in a comma-sepa

40、rated list).CLS:Number of columns in the file.RWS:Number of rows in the file.BTS:Number of bytes in the file.Table: SRFLDUMLS?FieldDescription【ererenceiMfnualDES:Description of the field.REF:Cross-reference to the documentation.FIL:File name(s) in which the field is found.Sample Relati onal RecordsS

41、RDEFSTY|T020|Acquired Abn ormality|A1.2.2.2|A n abn ormal structure, or one that is abn ormal in size or location, found in or deriving from a previously normal structure. Acquired abno rmalities are dist in guished from diseases even though they may result in pathological functioning (e.g., "h

42、ernias in carcerate").|Abscess of prostate; Hemorrhoids; Hern ia, Femoral; Varicose Vein s|STY|T047|Disease or Syndrome|B2.2.1.2.1|A condition which alters or interferes with a normal process, state, or activity of an organism. It is usually characterized by the abnormal UMLS? Reference Manuafu

43、nctioning of one or more of the host's systems, parts, or organs. Included here is a complex of symptoms descriptive of a disorder.|Diabetes Mellitus; Dump ing Syn drome; Malabsorpti on Syn dromes; Nephrotic Syn drome|A ny specific disease or syn drome that is modified by such modifiers as "

44、;acute", "pro Ion ged", etc. will also be assig ned to this type. If an an atomic abno rmality has a pathologic mani festati on, the n it will be give n this type as well as a type from the 'An atomical Abno rmality' hierarchy, e.g., "Diabetic Cataract" will be doubl

45、e-typed for this reas on .|ds yn|STY|T052|Activity|B1|A n operati on or series of operati ons that an orga nism or machi ne carries out or participates inSocial Planning; Expediti on s; In formati on Distributi on; Return Migratio n|Few con cepts will be assig ned to this broad type. Wherever possib

46、le, one of the more specific types from this hierarchy will be chose n. For con cepts assig ned to this type, the focus of in terest is on the activity. When the focus of in terest is the in dividual or group that is carrying out the activity, then a type from the 'Behavior' hierarchy will b

47、e chosen. In general, con cepts will not receive a type from both the 'Activity' and the 'Behavior' hierarchies.|UMLS? Refere neeSTY|T059|Laboratory Procedure|B1.3.1.1|A procedure, method, or tech ni que used to determine the composition, quantity, or concentration of a specimen, and

48、 which is carried out in a cli ni cal laboratory .In cluded here are procedures which measure the times and rates of reacti on s.|Blood Protein Electrophoresis; Radioim muno assay; Atheroge nic in dex calculati on | lbpr|RL|T173|adjace nt_to|R2.2|Close to, n ear or abutti ng ano ther physical un it

49、with no other structure of the same kind in terve ning. This in cludes adjoins, abuts, is con tiguous to, is juxtaposed, and is close to.|AD|adjace nt_to|RL|T151|affects|R3.1|Produces a direct effect on. Implied is the alteri ng or in flue ncing of an existi ng con diti on, state, situati on, or en

50、tity. This in cludes has a role in, alters, in flue nces, predisposes, catalyzes, stimulates, regulates, depresses, impedes, enhan ces, con tributes to, leads to, and modifies.|AF|affected_by|SRSTRAcquired Abno rmality|co-occurs_with|Injury or Pois onin g|D| UMLS? Refere nee Man uaAcquired Abn ormal

51、ity|isa|A natomical Abn ormality|D|Acquired Abno rmality|result_of|Behavior|D|Activity|isa|Eve nt|D|Age Group|isa|Group|D|SRSTRE1T020|T186|T190|T020|T186|T017|T020|T186|T072|T052|T186|T051|T052|T165|T090|T052|T165|T091|T100|T186|T096|T100|T186|T077|T100|T186|T071|UMLS? Refere nee Man ua：SRSTRE2Acqui

52、red Abno rmality|isa|A natomical Abno rmality|Acquired Abno rmality|isa|A natomical StructureAcquired Abno rmality|isa|E ntity|Acquired Abno rmality|isa|Physical Object|Acquired Abn ormality|afects|Amphibia n|Acquired Abn ormality|afects|A nimal|Acquired Abno rmality|affects|Archae on|Acquired Abno

53、rmality|affects|Bacterium|Acquired Abno rmality|affects|Bird|Acquired Abno rmality|afects|Cell Fun cti on|Acquired Abno rmality|affects|Eukaryote|Acquired Abn ormality|afects|Fish|Manu aAcquired Abno rmality|affects|Ge netic Function|Acquired Abn ormality|afects|Huma n|Acquired Abno rmality|affects|

54、F un gus|UMLS? Refere neeAcquired Abno rmality|affects|Mammal|Acquired Abno rmality|affects|Me ntal Process|Acquired Abno rmality|affects|Molecular Function|Acquired Abno rmality|affects|Orga n or Tissue Function|Acquired Abn ormality|afects|Orga nism Function|Acquired Abn ormality|afects|Orga nism|

55、Acquired Abnormality|affects|Physiologic Function|Acquired Abn ormality|afects|Pla nt|Acquired Abno rmality|affects|Reptile|Acquired Abno rmality|affects|Vertebrate|Acquired Abn ormality|afects|Virus| Activity|isa|Eve nt|Age Group|isa|C on ceptual En tity|Age Group|isa|E ntity|Age Group|isa|Group|UM

56、LS?Network ASCII Unit Record FormatThe file "SU" contains in dividual records for both sema ntic types and relati ons.Each record begins with a unique identifier field (UI) which contains the four character UI.These are of the form "T001", "T002", etc. Each field in a r

57、ecord begi ns on a new line and may con ti nue over several lin es. Some fields are opti on al.Sema ntic Type records contain the follow ing fields:FieldDescriptionUI:Unique Identifier of the Semantic Type.STY:Name of the Semantic Type.STN:Tree Number of the Semantic Type.DEF:Definition of the Seman

58、tic Type.EX:Examples of Metathesaurus concepts with this Semantic Type (optional field).QterencageMOnui atmantic Type assignment (optional field).NH:Semantic Type and its descendants allow the non-human flag (optional field).HL:Hierarchical links of the Semantic Type to its parent (isa) and its chil

59、dren (inverse_isa). If there are no hierarchical links, then the value <none> is assigned.HL:Hierarchical links of the Semantic Type to its parent (isa) and its children (inverse_isa). If there are no hierarchical links, then the value<none> is assigned.Relation records contain the follo

60、wing fields:FieldDescriptionUI:Unique Identifier of the Relation.RL:Name of the Relation.ABR:Abbreviation of the Relation.RIN:Name of the inverse of the Relation.RferergeMlumbirilkhe Relation.DEF:Definition of the Relation.INH:"N" if the relation is not inherited (optional field).HL:Hierarchical links of the Relation to its parent (isa) and its children (inverse_i