#!perl #use lib '..\lib'; use OWL::Simple::Parser; use File::Temp; use Test::More tests => 8; # turn off info for test use Log::Log4perl qw(:easy); Log::Log4perl->easy_init( $WARN ); # create temp file form _DATA_ to get a proper filename my $fh = File::Temp->new; $fh->printflush( do { local $/; } ); my $parser = OWL::Simple::Parser->new( owlfile => $fh->filename, synonym_tag => 'efo:alternative_term', definition_tag => 'efo:RANDOMTAG' ); ok( $parser->parse, 'Parser loads' ); ok( $parser->version() eq '2.5classified', 'Version found' ); ok( $parser->class_count() > 0, 'Classes count' ); ok( $parser->synonyms_count() > 0, 'Synonyms count' ); ok( $parser->class->{EFO_0000616}->definitions->[0], 'Found definitions on custom tag' ); ok( !defined $parser->class->{EFO_0000304}->definitions->[0], 'No definitions' ); ok( $parser->class->{EFO_0000616}->subClassOf->[0], 'Found child' ); # TEST the code from synopsis # iterate through all the classes for my $id (keys %{ $parser->class }){ my $OWLClass = $parser->class->{$id}; print $id . ' ' . $OWLClass->label . "\n"; # list synonyms for my $syn (@{ $OWLClass->synonyms }){ print "\tsynonym - $syn\n"; } # list definitions for my $def (@{ $OWLClass->definitions }){ print "\tdef - $def\n"; } # list parents for my $parent (@{ $OWLClass->subClassOf }){ print "\tsubClassOf - $parent\n"; } } pass('SYNOPSIS'); __DATA__ Bioportal mappings to Phenotypic quality (PATO) ver1.221 Bioportal mappings to BRENDA tissue / enzyme source (BTO) ver1.3 Bioportal mappings to Microarray experimental conditions (MO) ver1.3.1.1 Tomasz Adamusiak Bioportal mappings to Zebrafish anatomy and development (ZFA) ver1.27 Bioportal mappings to Units of measurement (UO) ver1.27 Bioportal mappings to SNOMED Clinical Terms (SNOMEDCT) ver2009_07_31 Bioportal mappings to NCBI organismal classification (null) ver1.2 Bioportal mappings to MGED Ontology (MO) ver1.3.1.1 Bioportal mappings to Human disease (DOID) ver1.192 2.5 classified Helen Parkinson Bioportal mappings to International Classification of Diseases (ICD-9) ver9 Mappings:The Arabidopsis Information Resource (TAIR) Bioportal mappings to Foundational Model of Anatomy (FMA) ver3.0 Bioportal mappings to Chemical entities of biological interest (CHEBI) ver1.66 Bioportal mappings to Minimal anatomical terminology (MAT) ver1.1 Mappings to Plant structure (PO) Mappings: CRISP Thesaurus Version 2.5.2.0 Bioportal mappings to Malaria Ontology (IDOMAL) ver1.1 Date: 1st July 2010: Bioportal mappings to Medical Subject Headings (MSH) ver2010_2009_08_17 Bioportal mappings to Mosquito gross anatomy (TGMA) ver1.10 Bioportal mappings to Gene Ontology (GO) ver1.886 James Malone Mappings: The Jackson Lab Bioportal mappings to Teleost anatomy and development (TAO) ver1.158 Bioportal mappings to NCI Thesaurus (NCIt) ver10.01 Bioportal mappings to Drosophila gross anatomy (FBbt) ver1.33 Bioportal mappings to Mammalian phenotype (MP) ver1.347 Ele Holloway Bioportal mappings to Ontology for Biomedical Investigations (OBI) ver2009-11-06 Philly (aka version 1.0) Release Candidate Bioportal mappings to NIFSTD (nif) ver1.8 Bioportal mappings to Cell type (CL) ver1.43 James Malone carcinoma A type of malignant cancer that arises from epithelial cells tending to infiltrate the surrounding tissues and give rise to metastases. James Malone disease A disease is a disposition that describes states of disease associated with a particular sample and/or organism. Neoplasia[accessedResource: NCIt:C3262][accessDate: 10-05-2010] An abnormal tissue growth resulted from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant ones exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias. NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS)[accessedResource: NCIt:C3262][accessDate: 10-05-2010] An abnormal tissue growth resulted from uncontrolled cell proliferation. neoplasm A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias.[accessedResource: NCIt:C3262][accessDate: 10-05-2010] Neoplastic Growth Tumor[accessedResource: NCIt:C3262][accessDate: 10-05-2010] Neoplasms Neoplastic Growth[accessedResource: NCIt:C3262][accessDate: 10-05-2010] James Malone NCIt:C3262 Neoplasms[accessedResource: NCIt:C3262][accessDate: 10-05-2010] Tumor A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias. Neoplasia NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) acinar cell carcinoma Acinic cell adenocarcinoma Acinic Cell Carcinoma GeneRIF:11891193 Carcinomas, Acinar Cell[accessedResource: MSH:D018267][accessDate: 10-05-2010] MSH:D018267 DOID:3025 Acinar carcinoma[accessedResource: SNOMEDCT:45410002][accessDate: 10-05-2010] Acinar Cell Carcinomas A malignant glandular epithelial neoplasm consisting of secretory cells forming acinar patterns. Representative examples include the acinar cell carcinoma of the pancreas and the acinar adenocarcinoma of the prostate gland. James Malone Acinar Adenocarcinoma Acinar Cell Adenocarcinoma[accessedResource: NCIt:C3768][accessDate: 10-05-2010] Acinar adenocarcinoma[accessedResource: SNOMEDCT:45410002][accessDate: 10-05-2010] Acinar Cell Adenocarcinoma A malignant glandular epithelial neoplasm consisting of secretory cells forming acinar patterns. Representative examples include the acinar cell carcinoma of the pancreas and the acinar adenocarcinoma of the prostate gland.[accessedResource: NCIt:C3768][accessDate: 10-05-2010] SNOMEDCT:45410002 acinar cell carcinoma (morphologic abnormality)[accessedResource: DOID:3025][accessDate: 10-05-2010] Acinic Cell Adenocarcinoma[accessedResource: NCIt:C3768][accessDate: 10-05-2010] A malignant tumor arising from secreting cells of a racemose gland, particularly the salivary glands. Racemose (Latin racemosus, full of clusters) refers, as does acinar (Latin acinus, grape), to small saclike dilatations in various glands. Acinar cell carcinomas are usually well differentiated and account for about 13% of the cancers arising in the parotid gland. Lymph node metastasis occurs in about 16% of cases. Local recurrences and distant metastases many years after treatment are common. This tumor appears in all age groups and is most common in women. (Stedman, 25th ed; Holland et al., Cancer Medicine, 3d ed, p1240; from DeVita Jr et al., Cancer: Principles & Practice of Oncology, 3d ed, p575)[accessedResource: MSH:D018267][accessDate: 10-05-2010] A malignant tumor arising from secreting cells of a racemose gland, particularly the salivary glands. Racemose (Latin racemosus, full of clusters) refers, as does acinar (Latin acinus, grape), to small saclike dilatations in various glands. Acinar cell carcinomas are usually well differentiated and account for about 13% of the cancers arising in the parotid gland. Lymph node metastasis occurs in about 16% of cases. Local recurrences and distant metastases many years after treatment are common. This tumor appears in all age groups and is most common in women. (Stedman, 25th ed; Holland et al., Cancer Medicine, 3d ed, p1240; from DeVita Jr et al., Cancer: Principles & Practice of Oncology, 3d ed, p575) Acinar carcinoma acinar cell carcinoma (morphologic abnormality) Acinic Cell Carcinoma[accessedResource: NCIt:C3768][accessDate: 10-05-2010] NCIt:C3768 Helen Parkinson MO_10 Helen Parkinson Tomasz Adamusiak Tomasz Adamusiak Concept naming convention is lower case natural naming with spaces, when necessary captials should be used, for example disease factor, HIV, breast carcinoma, Ewing's sarcoma Jie Zheng An experimental factor in Array Express. An experimental factor in Array Express which are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. James Malone James Malone experimental factor true Tomasz Adamusiak true malignant tumor malignant neoplasia James Malone malignant tumour cancer ductal carcinoma in situ NIFSTD:birnlex_406 A malignant neoplasm in which new abnormal tissue grow by excessive cellular division and proliferation more rapidly than normal and continues to grow after the stimuli that initiated the new growth cease. breast adenocarcinoma James Malone DOID:4468 [M]Clear cell adenocarcinoma NOS GeneRIF:15102668 SNOMEDCT:189633003 GeneRIF:15884099 clear cell adenocarcinoma GeneRIF:12937142 Mesonephroid Clear Cell Carcinoma clear cell carcinoma An adenocarcinoma characterized by the presence of varying combinations of clear and hobnail-shaped tumor cells. There are three predominant patterns described as tubulocystic, solid, and papillary. These tumors, usually located in the female reproductive organs, have been seen more frequently in young women since 1970 as a result of the association with intrauterine exposure to diethylstilbestrol. (From Holland et al., Cancer Medicine, 3d ed) Mesonephroid clear cell adenocarcinoma[accessedResource: SNOMEDCT:30546008][accessDate: 10-05-2010] [M]Clear cell adenocarcinoma NOS[accessedResource: SNOMEDCT:189633003][accessDate: 10-05-2010] GeneRIF:14559803 A malignant neoplasm composed of glandular epithelial clear cells. Various architectural patterns may be seen, including papillary, tubulocystic, and solid. Mesonephroid Clear cell carcinoma[accessedResource: DOID:4468][accessDate: 10-05-2010] A malignant neoplasm composed of glandular epithelial clear cells. Various architectural patterns may be seen, including papillary, tubulocystic, and solid.[accessedResource: NCIt:C3766][accessDate: 10-05-2010] MSH:D018262 Clear cell adenocarcinoma NOS (morphologic abnormality)[accessedResource: DOID:4468][accessDate: 10-05-2010] Clear cell adenocarcinoma, NOS Adenocarcinomas, Clear Cell[accessedResource: MSH:D018262][accessDate: 10-05-2010] Clear cell adenocarcinoma, NOS[accessedResource: SNOMEDCT:30546008][accessDate: 10-05-2010] [M]Clear cell adenocarcinoma NOS (morphologic abnormality) GeneRIF:15297970 GeneRIF:12086860 James Malone An adenocarcinoma characterized by the presence of varying combinations of clear and hobnail-shaped tumor cells. There are three predominant patterns described as tubulocystic, solid, and papillary. These tumors, usually located in the female reproductive organs, have been seen more frequently in young women since 1970 as a result of the association with intrauterine exposure to diethylstilbestrol. (From Holland et al., Cancer Medicine, 3d ed)[accessedResource: MSH:D018262][accessDate: 10-05-2010] Clear cell adenocarcinoma (morphologic abnormality)[accessedResource: DOID:4468][accessDate: 10-05-2010] GeneRIF:12970394 Clear cell adenocarcinoma NOS (morphologic abnormality) GeneRIF:14729622 Clear cell adenocarcinoma (morphologic abnormality) Mesonephroid clear cell adenocarcinoma GeneRIF:14722919 SNOMEDCT:30546008 NCIt:C3766 Clear cell carcinoma[accessedResource: SNOMEDCT:30546008][accessDate: 10-05-2010] GeneRIF:15489654 GeneRIF:14633622 Clear Cell Adenocarcinomas [M]Clear cell adenocarcinoma NOS (morphologic abnormality)[accessedResource: SNOMEDCT:189633003][accessDate: 10-05-2010] adenocarcinoma A type of carcinoma derived from glandular tissue or in which tumor cells form recognizable glandular structures. James Malone CRISP Thesaurus 2006, Term Number 2000-0386, http://crisp.cit.nih.gov/Thesaurus/00000107.htm Date accessed: 1st Novemeber 2007 Adenocarcinoma of Cervix Uteri[accessedResource: NCIt:C4029][accessDate: 10-05-2010] Adenocarcinoma of Cervix[accessedResource: NCIt:C4029][accessDate: 10-05-2010] Adenocarcinoma of Cervix Uteri Cervix Adenocarcinoma cervical adenocarcinoma DOID:3702 NCIt:C4029 James Malone An adenocarcinoma arising from the cervical epithelium. It accounts for approximately 15% of invasive cervical carcinomas. Increased numbers of sexual partners and human papilloma virus (HPV) infection are risk factors. Grossly, advanced cervical adenocarcinoma may present as an exophytic mass, an ulcerated lesion, or diffuse cervical enlargement. Microscopically, the majority of cervical adenocarcinomas are of the endocervical (mucinous) type. Adenocarcinoma of the Cervix Uteri Cervix Uteri Adenocarcinoma[accessedResource: NCIt:C4029][accessDate: 10-05-2010] Adenocarcinoma of the Cervix Uteri[accessedResource: NCIt:C4029][accessDate: 10-05-2010] Cervix Adenocarcinoma[accessedResource: NCIt:C4029][accessDate: 10-05-2010] Adenocarcinoma of the Cervix An adenocarcinoma arising from the cervical epithelium. It accounts for approximately 15% of invasive cervical carcinomas. Increased numbers of sexual partners and human papilloma virus (HPV) infection are risk factors. Grossly, advanced cervical adenocarcinoma may present as an exophytic mass, an ulcerated lesion, or diffuse cervical enlargement. Microscopically, the majority of cervical adenocarcinomas are of the endocervical (mucinous) type.[accessedResource: NCIt:C4029][accessDate: 10-05-2010] Adenocarcinoma of the Uterine Cervix Adenocarcinoma of the Cervix[accessedResource: NCIt:C4029][accessDate: 10-05-2010] Adenocarcinoma of Uterine Cervix[accessedResource: NCIt:C4029][accessDate: 10-05-2010] Uterine Cervix Adenocarcinoma[accessedResource: NCIt:C4029][accessDate: 10-05-2010] Adenocarcinoma of Uterine Cervix Adenocarcinoma of the Uterine Cervix[accessedResource: NCIt:C4029][accessDate: 10-05-2010] Cervix Uteri Adenocarcinoma Adenocarcinoma of Cervix Uterine Cervix Adenocarcinoma MSH:D002282 Bronchiolo-alveolar adenocarcinoma (morphologic abnormality)[accessedResource: SNOMEDCT:112677002][accessDate: 10-05-2010] Bronchioloalveolar Adenocarcinoma of the Lung[accessedResource: NCIt:C2923][accessDate: 10-05-2010] Carcinoma, Bronchiolar[accessedResource: MSH:D002282][accessDate: 10-05-2010] Alveolar adenocarcinoma (morphologic abnormality) Alveolar Adenocarcinomas [M]Bronchiolo-alveolar adenocarcinoma[accessedResource: SNOMEDCT:112677002][accessDate: 10-05-2010] Bronchioloalveolar Carcinomas[accessedResource: MSH:D002282][accessDate: 10-05-2010] Bronchiolo-Alveolar Carcinoma of Lung Bronchioloalveolar carcinoma - disorder Bronchiolo-Alveolar Carcinoma Carcinomas, Bronchiolo-Alveolar[accessedResource: MSH:D002282][accessDate: 10-05-2010] Bronchioloalveolar Lung Adenocarcinoma Bronchiolo-Alveolar Adenocarcinomas[accessedResource: MSH:D002282][accessDate: 10-05-2010] [M]Bronchiolo-alveolar adenocarcinoma Alveolar Adenocarcinoma[accessedResource: MSH:D002282][accessDate: 10-05-2010] Bronchioalveolar Adenocarcinoma of Lung[accessedResource: NCIt:C2923][accessDate: 10-05-2010] A carcinoma thought to be derived from epithelium of terminal bronchioles, in which the neoplastic tissue extends along the alveolar walls and grows in small masses within the alveoli. Involvement may be uniformly diffuse and massive, or nodular, or lobular. The neoplastic cells are cuboidal or columnar and form papillary structures. Mucin may be demonstrated in some of the cells and in the material in the alveoli, which also includes denuded cells. Metastases in regional lymph nodes, and in even more distant sites, are known to occur, but are infrequent. (From Stedman, 25th ed) A well or moderately differentiated morphologic variant of lung adenocarcinoma characterized by tumor growth along the alveolar structures without stromal, vascular, or pleural invasion.[accessedResource: NCIt:C2923][accessDate: 10-05-2010] A carcinoma thought to be derived from epithelium of terminal bronchioles, in which the neoplastic tissue extends along the alveolar walls and grows in small masses within the alveoli. Involvement may be uniformly diffuse and massive, or nodular, or lobular. The neoplastic cells are cuboidal or columnar and form papillary structures. Mucin may be demonstrated in some of the cells and in the material in the alveoli, which also includes denuded cells. Metastases in regional lymph nodes, and in even more distant sites, are known to occur, but are infrequent. (From Stedman, 25th ed)[accessedResource: MSH:D002282][accessDate: 10-05-2010] Bronchiolo-Alveolar Carcinoma[accessedResource: MSH:D002282][accessDate: 10-05-2010] Carcinoma, Bronchioloalveolar[accessedResource: MSH:D002282][accessDate: 10-05-2010] Carcinomas, Bronchioloalveolar Alveolar Carcinomas Bronchioloalveolar adenocarcinoma SNOMEDCT:373627005 Carcinomas, Bronchiolo-Alveolar SNOMEDCT:112677002 Alveolar Carcinomas[accessedResource: MSH:D002282][accessDate: 10-05-2010] Bronchiolo-Alveolar Lung Carcinoma[accessedResource: NCIt:C2923][accessDate: 10-05-2010] Alveolar Adenocarcinomas[accessedResource: MSH:D002282][accessDate: 10-05-2010] Bronchiolo-alveolar adenocarcinoma[accessedResource: SNOMEDCT:112677002][accessDate: 10-05-2010] Carcinomas, Bronchiolar NCIt:C2923 Bronchiolo-Alveolar Lung Carcinoma BAC[accessedResource: NCIt:C2923][accessDate: 10-05-2010] Bronchiolo-Alveolar Carcinoma of the Lung Bronchioloalveolar adenocarcinoma[accessedResource: DOID:4926][accessDate: 10-05-2010] BAC Bronchioloalveolar Adenocarcinoma of Lung Bronchioalveolar Adenocarcinoma of Lung James Malone Bronchiolo-Alveolar Carcinoma of Lung[accessedResource: NCIt:C2923][accessDate: 10-05-2010] Bronchiolo-Alveolar Adenocarcinomas Bronchioalveolar Lung Carcinoma Alveolar cell carcinoma[accessedResource: SNOMEDCT:112677002][accessDate: 10-05-2010] Alveolar adenocarcinoma (morphologic abnormality)[accessedResource: SNOMEDCT:36310008][accessDate: 10-05-2010] Bronchioloalveolar Lung Adenocarcinoma[accessedResource: NCIt:C2923][accessDate: 10-05-2010] Bronchioloalveolar Carcinoma Bronchioalveolar Adenocarcinoma of the Lung[accessedResource: NCIt:C2923][accessDate: 10-05-2010] Bronchiolar carcinoma Bronchioalveolar Lung Carcinoma[accessedResource: NCIt:C2923][accessDate: 10-05-2010] bronchoalveolar adenocarcinoma Alveolar cell carcinoma bronchiolo-alveolar adenocarcinoma Alveolar Adenocarcinoma A well or moderately differentiated morphologic variant of lung adenocarcinoma characterized by tumor growth along the alveolar structures without stromal, vascular, or pleural invasion. Bronchiolo-Alveolar Carcinoma of the Lung[accessedResource: NCIt:C2923][accessDate: 10-05-2010] Bronchiolar Carcinomas[accessedResource: MSH:D002282][accessDate: 10-05-2010] Alveolar carcinoma[accessedResource: SNOMEDCT:36310008][accessDate: 10-05-2010] Bronchioloalveolar Adenocarcinoma of the Lung DOID:4926 Bronchioloalveolar Adenocarcinoma of Lung[accessedResource: NCIt:C2923][accessDate: 10-05-2010] Bronchioloalveolar carcinoma (disorder)[accessedResource: DOID:4926][accessDate: 10-05-2010] Bronchioalveolar Adenocarcinoma of the Lung Bronchiolar adenocarcinoma[accessedResource: SNOMEDCT:112677002][accessDate: 10-05-2010] Alveolar Carcinoma Bronchiolo-alveolar adenocarcinoma (morphologic abnormality) SNOMEDCT:36310008 Bronchiolar adenocarcinoma Jie Zheng James Malone organization An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. MO_177 organisation http://www.ebi.ac.uk/efo/EFO_0002010 Tomasz Adamusiak James Malone A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray. material entity An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. true sample factor http://www.ebi.ac.uk/efo/EFO_0001434 A heart, a human, a fly, a microarray. material property SpecificallyDependentContinuant James Malone true An experimental factor which is a property or characteristic of some other entity. For example, the mouse has the colour white. sample characteristic A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. http://www.ebi.ac.uk/efo/EFO_0001443 James Malone A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C. http://www.ebi.ac.uk/efo/EFO_0001438 For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease. A disposition is an entity that essentially causes a specific process or transformation in an entity in which it inheres, under specific circumstances and in conjunction with the laws of nature. For example, the disposition of vegetables to decay when not refrigerated, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease. disease property true disposition is_input_of http://www.ebi.ac.uk/efo/is_input_of contained_in http://www.ebi.ac.uk/efo/contained_in Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. http://www.ebi.ac.uk/efo/location_of location_of http://www.ebi.ac.uk/efo/realizes realizes Relation between a process and a material fulfilling a role (i.e. realizing a role within the context of the process). For example a human realizing role of teacher within a lesson teching process. is_location_of_disease has_input http://www.ebi.ac.uk/efo/has_input http://www.ebi.ac.uk/efo/EFO_0000829 inheres_in http://www.ebi.ac.uk/efo/EFO_0001377 A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in [GOC:cjm] example of usage: red eye bearer_of redness bearer_of is_unit_of http://www.ebi.ac.uk/efo/derives_from derives_from Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant. has_disease_location is_broader_than http://www.ebi.ac.uk/efo/contains contains Participates in is a primitive instance-level relation between a continuant and a process in which it participates. For example a scanner participates in a scanning process at some specific time. participates_in part_of For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) EFO_0000822 http://www.ebi.ac.uk/efo/part_of derived_into http://www.ebi.ac.uk/efo/derived_into has_tumor_type has_part EFO_0000823 http://www.ebi.ac.uk/efo/has_part is_realized_by Relation between a realizable entity and a process. Reciprocal relation of realizes http://www.ebi.ac.uk/efo/is_realized_by role_of http://www.ebi.ac.uk/efo/is_role_of http://www.ebi.ac.uk/efo/located_in located_in has_unit relationship has_participant Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the A continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_role A relation between a continuant C and a role R. The reciprocal relation of role_of. http://www.ebi.ac.uk/efo/has_role http://www.ebi.ac.uk/efo/has_quality has_quality is_tumor_of ENCODE James Malone ENCODE, full name the Encyclopedia Of DNA Elements, is a public research consortium which has the aim of identifying all functional elements in the human genome sequence. ENCODE website <http://www.genome.gov/10005107> The International HapMap Project Tha HapMap Project webpage <http://hapmap.ncbi.nlm.nih.gov> The International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals. James Malone