Ontology of Pathological Structures

Transcription

1 ntology of Pathological Structures apping the Human Body SU at Buffalo, nand Kumar BBS, Ph FS, epartment of edicine, Univ. of Saarland, ermany.

2 iological ntity classification using Realism natomic Structure (rgan system, rgan ) ndependent Biological Body ontinuant Substance(F: aterial natomic ntity) Biological ontinuants ependent natomical ontinuant ependent (F: mmaterial Biological natomical ontinuant entity point, space, surface, line) ependent Physiological ontinuant (function) Biological ntity Biological ccurants (processes, events, actions)

3 umor, ode, etastasis () lassification l definition evel of ranularity ther partitions is arcinoma in situ: intraepithelial or invasion of the lamina propria ntraepithelial cell (); pithelium & lamina propria (RP/P) 1 umor invades submucosa Submucosa of colon (RP/P) 2 umor invades muscularis propria uscularis mucosa of colon (RP/P) 3 umor invades through the muscularis propria into the subserosa, or into nonperitonealized pericolic or perirectal tissues Subserosa of colon (RP/P), nonperitonealized pericolic or perirectal tissues (RP/P-) path of invasion (pathogenesis) 4 umor directly invades other organs or structures, and/or perforates visceral peritoneum organs (R-), visceral peritoneum (RP) path of invasion (pathogenesis) 0 o regional lymph node metastasis -- 1 etastasis in 1 to 3 regional lymph nodes lymph node (RP), collection of lymph nodes (RP-) number 2 etastasis in 4 or more regional lymph nodes lymph node (RP), collection of lymph nodes (RP-) number 0 o distant metastasis -- 1 istant metastasis R

4 Problems with ontologies of Pathological structures ndescent anatomy: hesaurus olon part-of arge ntestine olon synonym arge ntestine Snomed : mputation of leg is-a mputation of any part of lower limb, including total amputation SP classification: lfa proteins, Beta proteins, membranous proteins etc.

5 Problems with ontologies of Pathological structures Unclear distinctions between pathological structure, stage and disease a. 210 stage of colon carcinoma b. 210 stage colon carcinoma structure c. olon carcinoma disease with 210 stage colon carcinoma structure nadequate representation of time 210 stage colon carcinoma structure preceded by 110 stage colon carcinoma structure preceded by 100 stage colon carcinoma structure preceded by normal colon

6 Problems with ontologies of Pathological structures nadequate distinction between instance and classes 210 stage colon carcinoma structure preceded by 110 stage colon carcinoma structure? or 210 stage colon carcinoma structure preceded by 200 stage colon carcinoma structure? onfusions over relation between normal and abnormal structures olon with carcinoma is a olon? ompletely cirrhotic liver is a iver? ucosa of colon with complete rohn s disease is a ucosa of colon?

7 211 colon carcinoma structure Processes involved 2: umor invades muscularis propria 1: etastasis in 1 to 3 lymph nodes 1: istant metastasis Pathological structures 211 colon carcinoma pathological structure: 2 colon carcinoma pathological structure implies Portion of colon mucosa carcinoma pathological structure and Portion of colon submucosa carcinoma pathological structure and Portion of colon muscularis propria carcinoma structure

8 211 colon carcinoma structure 2 colon carcinoma structure implies 1 lymph node with colon carcinoma metastatic structure or 2 lymph node with colon carcinoma metastatic structure or 3 lymph node with colon carcinoma metastatic structure 1 colon carcinoma structure implies ung with colon carcinoma metastatic structure or iver with colon carcinoma metastatic structure or. 211 colon carcinoma structure is a ollection of pathological structures

9 211 colon carcinoma structure 211 colon carcinoma structure has-member 2 colon carcinoma structure and has-member 1 colon carcinoma structure and has-member 1 colon carcinoma structure 211 colon carcinoma process: is constituted by abnormal processes associated with the carcinoma development 211 colon carcinomatous process has-part 2 colon carcinomatous process and has-part 1 colon carcinomatous process and has-part 1 colon carcinomatous process

10 nstance of 211 colon carcinoma structure inst(211 carcinoma structure) implies mucosal carcinoma structure and muscularis mucosal carcinoma structure and 3 paracolic lymph nodal metastatic structure and left upper lung lobe metastatic structure 211 carcinomatous structure transformation_of 210 carcinomatous structure transformation_of 200 carcinomatous structure transformation_of 100 carcinomatous structure transformation_of is00 carcinomatous structure transformation_of olon part

11 nstance of 211 colon carcinoma structure left upper lung metastatic carcinomatous process preceded-by distant organ metastasis preceded-by paracolic lymph nodal carcinomatous process preceded-by lymph nodal metastasis preceded-by muscularis proprial carcinomatous process preceded-by trans-submucosal carcinomatous invasion preceded-by submucosal carcinomatous process preceded-by transmucosal carcinomatous invasion preceded-by mucosal carcinomatous process preceded-by transcellular carcinomatous process preceded-by epithelial cellular carcinomatous process

12 211 colon carcinoma processes: lass level Process workflow which is always true: 4 colon carcinomatous process preceded-by 3 colon carcinomatous process preceded-by 2 colon carcinomatous process preceded-by 1 colon carcinomatous process preceded-by is colon carcinomatous process 2 colon carcinomatous process preceded-by 1 colon carcinomatous process preceded-by 0 colon carcinomatous process 1 colon carcinomatous process preceded-by 0 colon carcinomatous process

13 211 colon carcinoma processes: lass level 421 implies preceded-by (321 or 411 or 420) 321 implies preceded-by (221 or 311 or 320) xyz implies preceded-by (x-1yz or xy-1z or xyz-1) where 4 = x = 1 and 2 y 0 and 1 z 0 is colon carcinoma structure can only coexist with 0 colon carcinoma structure and 0 colon carcinoma structure; and accordingly the processes

14 evels of granularity natomical levels of granularity in human body: rganism rgan system / ardinal body part rgan rgan part / aximum portion of tissue ell Sub-cellular organelle olecule tom Fundamentals behind the levels: rains, Structure, rigin

15 Results from database-approach B R binding nucleus 30 binding nucleosome 31 transcriptional activator activity nucleus 31 structural constituent of ribosome cytosolic large ribosomal subunit (sensu ukarya) 32 transmembrane receptor activity integral to plasma membrane 36 protein binding cytoplasm 36 zinc ion binding nucleus 43 protein binding nucleus 45 receptor activity integral to plasma membrane 56 -protein coupled receptor activity integral to plasma membrane 70 binding nucleus 100 antigen binding extracellular 123 transcription factor activity nucleus 171

16 Finer levels of granularity Where are the cells with such abnormalities located? ot the ulcer ot the necrotic portion ot in the blood vessels, lymphatic vessels which feed into colon carcinoma structure Such abnormalities exist within the living cancerous cells ucosal ulcer implies not (portion of mucosa) and ulcer margin and ulcer shape and

17 Finer levels of granularity olon with 211 carcinoma and necrotic mucosal ulcer implies. and not (portion of colon mucosa) and necrotic tissue derived from portion of colon mucosa and cancerous portion of colon mucosa absent portion of colon mucosa is like unicorn ot a universal haracteristics of cancerous cells do not exist in the bsent portion of mucosa as there are no mucosal cells there haracteristics of cancerous cells do not exist in the normal portion of mucosa as there are no cancerous cells there

18 Finer levels of granularity bnormalities which are represented in ene ntology nnotations, Pathways/Portions/Quantitative representations active in carcinomas in Reactome, Protein-protein interactions present in ntct, P, B for such pathways are located in complete portion of mucosa olon with 211 colon carcinoma structure and necrotic mucosal ulcer is-a olon HS entity does not have all cells / all portions of tissue / organ parts which RHS entity has HS entity has some more cells / portions of tissue / organ parts which RHS entity has

19 ntology of pathological structures e Biology Workshop,, okyo 11. arch 2005 nand Kumar BBS, Ph FS, epartment of edicine, Univ. of Saarland, ermany.