From: Seth C. <sjc...@us...> - 2013-02-09 09:24:03
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Update of /cvsroot/obo/obo/ontology/phenotype In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv4151/phenotype Modified Files: mammalian_phenotype.obo transmission_process.obo Log Message: Automated file update Index: transmission_process.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/transmission_process.obo,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -d -r1.17 -r1.18 *** transmission_process.obo 31 Dec 2012 09:11:43 -0000 1.17 --- transmission_process.obo 9 Feb 2013 09:24:00 -0000 1.18 *************** *** 1,173 **** - format-version: 1.0 - date: 06:02:2008 14:52 - saved-by: Lynn - auto-generated-by: OBO-Edit 1.101 - default-namespace: transmission_process - - [Term] - id: TRANS:0000000 - name: transmission process - def: "A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host." [URL:http\://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf] - - [Term] - id: TRANS:0000001 - name: direct - def: "Direct transmission is a transmission process that is the means during which the pathogen is transmitted immediately from a reservoir, source or host to another host." [Gemina:lschriml "Lynn Schriml <lsc...@so...>", URL:http\://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf] - is_a: TRANS:0000000 ! transmission process - - [Term] - id: TRANS:0000002 - name: indirect - def: "Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles." [Gemina:lschriml "Lynn Schriml <lsc...@so...>", URL:http\://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf] - is_a: TRANS:0000000 ! transmission process - - [Term] - id: TRANS:0000003 - name: mechanical - def: "Mechanical transmission is an indirect vector-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by being transported on the external surface of the vector." [REF:lschriml "Lynn Schriml <lsc...@so...>"] - is_a: TRANS:0000005 ! vector-borne - - [Term] - id: TRANS:0000004 - name: unknown - is_obsolete: true - - [Term] - id: TRANS:0000005 - name: vector-borne - def: "Vector-borne transmission is an indirect transmission process during which the pathogen is indirectly transferred from a reservoir, source or host via an animate intermediary vector to another host. Most vectors are arthropods such as mosquitoes, fleas, and ticks." [REF:lschriml "Lynn Schriml <lsc...@so...>", URL:http\://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf] - is_a: TRANS:0000002 ! indirect - - [Term] - id: TRANS:0000006 - name: congenital - def: "Congenital transmission is a direct transmission process during which the pathogen is transmitted directly from mother to child at or around the time of birth." [Gemina:lschriml "Lynn Schriml <lsc...@so...>", URL:http\://www.m-w.com/dictionary/congenital] - exact_synonym: "mother-to-child transmission" [] - is_a: TRANS:0000001 ! direct - - [Term] - id: TRANS:0000007 - name: contact - def: "Contact transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by kissing, skin-to-skin contact, sexual intercourse, or by contact with soil or vegetation containing the pathogen." [REF:lschriml "Lynn Schriml <lsc...@so...>"] - is_a: TRANS:0000001 ! direct - - [Term] - id: TRANS:0000008 - name: droplet spread - def: "Droplet spread transmission is a direct transmission process during which the pathogen is transmitted from a reservoir, source or host to another host by spray of aerosols over a short distance, spray from sneezing, coughing or talking." [REF:lschriml "Lynn Schriml <lsc...@so...>"] - is_a: TRANS:0000001 ! direct - - [Term] - id: TRANS:0000009 - name: airborne - def: "Airborne transmission is an indirect transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host while suspended in the air as dust." [REF:lschriml "Lynn Schriml <lsc...@so...>"] - is_a: TRANS:0000002 ! indirect - - [Term] - id: TRANS:0000010 - name: vehicle-borne - def: "Vehicle-borne transmission is an indirect transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by inanimate intermediary vehicle objects." [REF:lschriml "Lynn Schriml <lsc...@so...>", URL:http\://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf] - is_a: TRANS:0000002 ! indirect - - [Term] - id: TRANS:0000011 - name: vehicle-borne fomite - def: "Vehicle-borne fomite transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by inanimate objects including: medical instruments, cloth, fur, metal or plastic utensils." [REF:lschriml "Lynn Schriml <lsc...@so...>"] - is_a: TRANS:0000010 ! vehicle-borne - - [Term] - id: TRANS:0000012 - name: vehicle-borne ingestion - def: "Vehicle-borne ingestion transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by ingestion of fluids or foods or food products including: food, water, milk, or meat products." [REF:lschriml "Lynn Schriml <lsc...@so...>"] - is_a: TRANS:0000010 ! vehicle-borne - - [Term] - id: TRANS:0000013 - name: vehicle-borne medical - def: "Vehicle-borne medical transmission is an indirect vehicle-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by biological products including: blood, serum, plasma, tissue, or organs." [REF:lschriml "Lynn Schriml <lsc...@so...>"] - is_a: TRANS:0000010 ! vehicle-borne - - [Term] - id: TRANS:0000014 - name: vector-borne bite - def: "Vector-borne bite transmission is an indirect vector-borne transmission during which the pathogen is indirectly transferred by insect bites from a reservoir, source or host via a vector to another host." [REF:lschriml "Lynn Schriml <lsc...@so...>"] - is_a: TRANS:0000005 ! vector-borne - - [Term] - id: TRANS:0000015 - name: vector-borne gastro-intestinal - def: "Vector-borne gastro-intestinal transmission is an indirect vector-borne transmission process during which the pathogen is transported, from a reservoir, source or host to another host, within the vector and undergoes part of it's lifecycle in the intermediate host." [REF:lschriml "Lynn Schriml <lsc...@so...>"] - exact_synonym: "biologic transmission" [] - is_a: TRANS:0000005 ! vector-borne - - [Term] - id: TRANS:0000016 - name: undocumented - is_obsolete: true - - [Term] - id: TRANS:0000017 - name: not curated - is_obsolete: true - - [Term] - id: TRANS:0000018 - name: placental - def: "Placental transmission is a congenital transmission process during which the pathogen is transmitted directly from mother to child across the placental barrier." [REF:lschriml "Lynn Schriml <lsc...@so...>", URL:http\://www.nlm.nih.gov/medlineplus/mplusdictionary.html] - is_a: TRANS:0000006 ! congenital - - [Term] - id: TRANS:0000019 - name: arthropod borne - def: "Arthropod borne transmission is a vector-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host via an animate intermediary arthropod vector to another host." [Gemina:lschriml "Lynn Schriml <lsc...@so...>", URL:http\://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf] - is_a: TRANS:0000005 ! vector-borne - - [Term] - id: TRANS:0000020 - name: insect borne - def: "Insect borne transmission is an arthropod vector-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host via an intermediary insect vector such as a flea or mosquito to another host." [Gemina:lschriml "Lynn Schriml <lsc...@so...>", URL:http\://www.cals.ncsu.edu/course/ent425/text18/humanvectors.html] - is_a: TRANS:0000019 ! arthropod borne - - [Term] - id: TRANS:0000021 - name: mosquito borne - def: "Mosquito borne transmission is an insect borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host via an intermediary mosquito vector to another host." [Gemina:lschriml "Lynn Schriml <lsc...@so...>", wiki:http\://en.wikipedia.org/wiki/Mosquito] - is_a: TRANS:0000020 ! insect borne - - [Term] - id: TRANS:0000022 - name: Anopheles gambiae borne - def: "Anopheles gambiae borne transmission is a mosquito borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host via an intermediary mosquito vector of the species Anopheles gambiae to another host." [Gemina:lschriml "Lynn Schriml <lsc...@so...>", wiki:http\://en.wikipedia.org/wiki/Mosquito] - is_a: TRANS:0000021 ! mosquito borne - - [Term] - id: TRANS:0000023 - name: flea borne - def: "Flea borne transmission is an insect borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host via an intermediary flea vector to another host." [Gemina:lschriml "Lynn Schriml <lsc...@so...>", wiki:http\://en.wikipedia.org/wiki/Flea] - is_a: TRANS:0000020 ! insect borne - - [Term] - id: TRANS:0000024 - name: tick borne - def: "Tick borne transmission is an arachnid borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host via an intermediary tick vector to another host." [Gemina:lschriml "Lynn Schriml <lsc...@so...>", wiki:http\://en.wikipedia.org/wiki/Tick, wiki:http\://en.wikipedia.org/wiki/Vector_%28disease%29] - is_a: TRANS:0000027 ! arachnid borne - - [Term] - id: TRANS:0000025 - name: copepod borne - def: "Copepod borne transmission is a vector-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host via an animate intermediary copepod vector to another host." [Gemina:lschriml "Lynn Schriml <lsc...@so...>", URL:http\://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf] - is_a: TRANS:0000015 ! vector-borne gastro-intestinal - - [Term] - id: TRANS:0000026 - name: Dracunculus medinensis borne - def: "Dracunculus medinensis borne transmission is a copepod borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host via an animate intermediary copepod vector of the species Dracunculus medinensis to another host." [Gemina:lschriml "Lynn Schriml <lsc...@so...>", URL:http\://www2a.cdc.gov/phtn/catalog/pdf-file/Epi_Course.pdf] - exact_synonym: "Guinea worm borne" [] - is_a: TRANS:0000025 ! copepod borne - - [Term] - id: TRANS:0000027 - name: arachnid borne - def: "Arachnid borne transmission is an arthropod vector-borne transmission process during which the pathogen is indirectly transferred from a reservoir, source or host via an intermediary arthropod vector such as a tick to another host." [Gemina:lschriml "Lynn Schriml <lsc...@so...>", wiki:http\://en.wikipedia.org/wiki/Vector_%28disease%29] - is_a: TRANS:0000019 ! arthropod borne - --- 0 ---- Index: mammalian_phenotype.obo =================================================================== RCS file: /cvsroot/obo/obo/ontology/phenotype/mammalian_phenotype.obo,v retrieving revision 1.463 retrieving revision 1.464 diff -C2 -d -r1.463 -r1.464 *** mammalian_phenotype.obo 5 Jan 2013 09:15:18 -0000 1.463 --- mammalian_phenotype.obo 9 Feb 2013 09:23:56 -0000 1.464 *************** *** 1,4 **** format-version: 1.2 ! date: 21:12:2012 16:15 saved-by: csmith auto-generated-by: OBO-Edit 2.1 --- 1,4 ---- format-version: 1.2 ! date: 05:02:2013 15:39 saved-by: csmith auto-generated-by: OBO-Edit 2.1 *************** *** 9014,9017 **** --- 9014,9018 ---- def: "increased distance between the eyes" [ISBN:0-683-40008-8] synonym: "increased inner canthal distance" EXACT [] + synonym: "increased intercanthal distance" RELATED [] synonym: "wide set eyes" EXACT [] synonym: "wider inner canthal distance" EXACT [] *************** *** 21984,21989 **** synonym: "thrombocytopenia" EXACT [] synonym: "thrombopenia" EXACT [] - is_a: MP:0004720 ! abnormal platelet morphology is_a: MP:0011182 ! decreased hematopoietic cell number [Term] --- 21985,21990 ---- synonym: "thrombocytopenia" EXACT [] synonym: "thrombopenia" EXACT [] is_a: MP:0011182 ! decreased hematopoietic cell number + is_a: MP:0011898 ! abnormal platelet cell number [Term] *************** *** 28880,28883 **** --- 28881,28885 ---- name: decreased circulating iron level def: "less than the normal concentration of iron in the blood" [MGI:anna] + comment: Serum iron measures the total amount of iron in the blood, nearly all of which is bound to transferrin. subset: Europhenome_Terms subset: Sanger_Terms *************** *** 28892,28895 **** --- 28894,28898 ---- name: abnormal circulating iron level def: "anomalous blood concentration of the metallic element that normally occurs in the heme of hemoglobin, myoglobin, transferrin, ferritin, and iron-containing porphyrins; it is an essential component of enzymes such as catalase, peroxidase, and various cytochromes" [ISBN:0-683-40008-8] + comment: Serum iron measures the total amount of iron in the blood, nearly all of which is bound to transferrin. is_a: MP:0001770 ! abnormal iron level is_a: MP:0006357 ! abnormal circulating mineral level *************** *** 39016,39021 **** synonym: "increased thrombocyte number" RELATED [] synonym: "thrombocytosis" EXACT [] - is_a: MP:0004720 ! abnormal platelet morphology is_a: MP:0011181 ! increased hematopoietic cell number [Term] --- 39019,39024 ---- synonym: "increased thrombocyte number" RELATED [] synonym: "thrombocytosis" EXACT [] is_a: MP:0011181 ! increased hematopoietic cell number + is_a: MP:0011898 ! abnormal platelet cell number [Term] *************** *** 39449,39453 **** synonym: "hypoproteinemia" EXACT [] synonym: "reduced circulating total protein level" EXACT [] ! is_a: MP:0005416 ! abnormal circulating protein level [Term] --- 39452,39456 ---- synonym: "hypoproteinemia" EXACT [] synonym: "reduced circulating total protein level" EXACT [] ! is_a: MP:0011888 ! abnormal circulating total protein level [Term] *************** *** 39460,39464 **** synonym: "increased plasma total protein level" EXACT [] synonym: "increased total protein level" EXACT [] ! is_a: MP:0005416 ! abnormal circulating protein level [Term] --- 39463,39467 ---- synonym: "increased plasma total protein level" EXACT [] synonym: "increased total protein level" EXACT [] ! is_a: MP:0011888 ! abnormal circulating total protein level [Term] *************** *** 41682,41685 **** --- 41685,41691 ---- name: ocular hypotelorism def: "the distance between the eyes is reduced" [MGI:smb, NCBI:matt] + synonym: "close set eyes" RELATED [] + synonym: "decreased inner canthal distance" RELATED [] + synonym: "decreased intercanthal distance" RELATED [] is_a: MP:0001299 ! abnormal eye distance/ position *************** *** 50744,50747 **** --- 50750,50754 ---- def: "greater than the expected number of an adenocarcinoma arising from cells of the pancreas that secrete digestive enzymes, occurring in a specific population in a given time period" [MGI:csmith] synonym: "acinar carcinoma" RELATED [] + synonym: "increased pancreatic acinar cell adenocarcinoma incidence" EXACT [] synonym: "pancreatic ACC" EXACT [] synonym: "pancreatic acinar carcinoma" EXACT [] *************** *** 50749,50752 **** --- 50756,50760 ---- is_a: MP:0002038 ! carcinoma is_a: MP:0009153 ! increased pancreas tumor incidence + is_a: MP:0009308 ! adenocarcinoma [Term] *************** *** 50993,50996 **** --- 51001,51005 ---- name: increased circulating iron level def: "elevation in the concentration of iron in the blood" [MGI:smb] + comment: Serum iron measures the total amount of iron in the blood, nearly all of which is bound to transferrin. subset: Europhenome_Terms subset: Sanger_Terms *************** *** 80287,80290 **** --- 80296,80442 ---- creation_date: 2012-12-21T04:04:14Z + [Term] + id: MP:0011885 + name: abnormal circulating lipase level + def: "any anomaly in the concentration of lipase in the blood, in particular the serum; the measurement of serum lipase activity is widely used for the diagnosis of acute pancreatitis" [MGI:csmith] + is_a: MP:0001570 ! abnormal circulating enzyme level + created_by: csmith + creation_date: 2013-02-05T12:38:38Z + + [Term] + id: MP:0011886 + name: increased circulating lipase level + def: "elevated blood level of lipase in the blood, in particular the serum" [MGI:csmith] + is_a: MP:0011885 ! abnormal circulating lipase level + created_by: csmith + creation_date: 2013-02-05T12:39:39Z + + [Term] + id: MP:0011887 + name: decreased circulating lipase level + def: "reduced blood level of lipase in the blood, in particular the serum" [MGI:csmith] + is_a: MP:0011885 ! abnormal circulating lipase level + created_by: csmith + creation_date: 2013-02-05T12:39:39Z + + [Term] + id: MP:0011888 + name: abnormal circulating total protein level + def: "total serum protein concentration is outside the normal range" [RGD:cur] + is_a: MP:0005416 ! abnormal circulating protein level + created_by: csmith + creation_date: 2013-02-05T12:43:42Z + + [Term] + id: MP:0011889 + name: abnormal circulating ferritin level + def: "deviation from the normal concentration of ferritin, a ubiquitous intracellular protein that stores iron and releases it in a controlled fashion; some ferritin is also found in the blood and is measured in tests for overall iron levels, anemia and chronic diseases" [MGI:csmith] + is_a: MP:0005416 ! abnormal circulating protein level + created_by: csmith + creation_date: 2013-02-05T12:48:53Z + + [Term] + id: MP:0011890 + name: increased circulating ferritin level + def: "elevated concentration in the blood of ferritin, a ubiquitous intracellular protein that stores iron and releases it in a controlled fashion; some ferritin is also found in the blood and is measured in tests for overall iron levels, anemia and chronic diseases" [MGI:csmith] + is_a: MP:0011889 ! abnormal circulating ferritin level + created_by: csmith + creation_date: 2013-02-05T12:49:53Z + + [Term] + id: MP:0011891 + name: decreased circulating ferritin level + def: "reduced concentration in the blood of ferritin, a ubiquitous intracellular protein that stores iron and releases it in a controlled fashion; some ferritin is also found in the blood and is measured in tests for overall iron levels, anemia and chronic diseases" [MGI:csmith] + is_a: MP:0011889 ! abnormal circulating ferritin level + created_by: csmith + creation_date: 2013-02-05T12:49:53Z + + [Term] + id: MP:0011892 + name: abnormal circulating transferrin level + def: "deviation from the normal concentration in the blood of a plasma protein that reversibly binds and transports iron and other metal ions through the blood to the liver, spleen and bone marrow" [MGI:csmith] + is_a: MP:0005416 ! abnormal circulating protein level + created_by: csmith + creation_date: 2013-02-05T12:53:05Z + + [Term] + id: MP:0011893 + name: increased circulating transferrin level + def: "elevated concentration in the blood of a plasma protein that reversibly binds and transports iron and other metal ions through the blood to the liver, spleen and bone marrow" [MGI:csmith] + is_a: MP:0011892 ! abnormal circulating transferrin level + created_by: csmith + creation_date: 2013-02-05T12:54:01Z + + [Term] + id: MP:0011894 + name: decreased circulating transferrin level + def: "reduced concentration in the blood of a plasma protein that reversibly binds and transports iron and other metal ions through the blood to the liver, spleen and bone marrow" [MGI:csmith] + is_a: MP:0011892 ! abnormal circulating transferrin level + created_by: csmith + creation_date: 2013-02-05T12:54:01Z + + [Term] + id: MP:0011895 + name: abnormal circulating unsaturated transferrin level + def: "any anomaly in the concentration of transferrin that is not saturated (bound) with iron; this represents the reserve capacity of transferrin and is often measured by the Unsaturated Iron Binding Capacity (UIBC) test" [MGI:csmith] + synonym: "abnormal unsaturated iron binding capacity" EXACT [] + is_a: MP:0011892 ! abnormal circulating transferrin level + created_by: csmith + creation_date: 2013-02-05T01:52:06Z + + [Term] + id: MP:0011896 + name: increased circulating unsaturated transferrin level + def: "increase in the concentration of transferrin that is not saturated (bound) with iron; this represents the reserve capacity of transferrin and is often measured by the Unsaturated Iron Binding Capacity (UIBC) test" [MGI:csmith] + synonym: "increased unsaturated iron binding capacity" EXACT [] + is_a: MP:0011893 ! increased circulating transferrin level + is_a: MP:0011895 ! abnormal circulating unsaturated transferrin level + created_by: csmith + creation_date: 2013-02-05T01:52:06Z + + [Term] + id: MP:0011897 + name: decreased circulating unsaturated transferrin level + def: "reduction in the concentration of transferrin that is not saturated (bound) with iron; this represents the reserve capacity of transferrin and is often measured by the Unsaturated Iron Binding Capacity (UIBC) test" [MGI:csmith] + synonym: "decreased unsaturated iron binding capacity" RELATED [] + is_a: MP:0011894 ! decreased circulating transferrin level + is_a: MP:0011895 ! abnormal circulating unsaturated transferrin level + created_by: csmith + creation_date: 2013-02-05T01:52:06Z + + [Term] + id: MP:0011898 + name: abnormal platelet cell number + def: "anomaly in the normal numbers of the non-nucleated cells found in the blood and involved in blood coagulation" [MGI:csmith] + synonym: "abnormal thrombocyte cell number" EXACT [] + is_a: MP:0011180 ! abnormal hematopoietic cell number + created_by: csmith + creation_date: 2013-02-05T02:12:57Z + + [Term] + id: MP:0011899 + name: podocyte vacuolization + def: "abnormal presence of cavities or fluid-filled vesicles in the cytoplasm of the modified epithelial cell of the visceral layer of the Bowman capsule in the renal corpuscle, often indicative of podocyte injury" [MGI:anna] + synonym: "glomerular epithelial cell vacuolation" EXACT [] + synonym: "glomerular epithelial cell vacuolization" EXACT [] + synonym: "podocyte vacuolation" EXACT [] + synonym: "podocyte vacuoles" EXACT [] + synonym: "vacuolated podocytes" EXACT [] + synonym: "vacuolization of visceral epithelial cells" BROAD [] + synonym: "vacuolized podocytes" EXACT [] + is_a: MP:0005326 ! abnormal podocyte morphology + created_by: csmith + creation_date: 2013-02-05T03:15:15Z + + [Term] + id: MP:0011900 + name: podocyturia + def: "presence of kidney podocytes, their cell fragments, or podocyte-specific proteins in the urine; urinary loss of viable podocytes may serve as a diagnostic tool for pre-eclampsia and as a marker of active renal disease" [MGI:anna] + synonym: "urinary podocyte excretion" EXACT [] + synonym: "urinary podocytes" EXACT [] + is_a: MP:0009643 ! abnormal urine homeostasis + created_by: csmith + creation_date: 2013-02-05T03:26:54Z + [Typedef] id: part_of |