GATACA

Credits

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Data

Data - ToppGene Sources

The vast majority of all data in Gataca is from ToppGene so its credits cover data sources that are used within Gataca. The primary reason for utilizing the same sources between these applications is to help ensure consistancy between them. ToppGene, and Gataca, uses data from over 20 sources.

For ToppGene Credits, please visit:

ToppGene Links (Credits)

Data - GUDMAP

GUDMAP

The GUDMAP data within Gataca is only availble within the GUDMAP interface:

Gataca's GUDMAP

Data - UMLSKS

UMLSKS website

Software

Software - Solr

Solr website

Software - PrototypeJS

Prototype JS website

Prototype JavaScript framework, version 1.7
(c) 2005-2010 Sam Stephenson
 
Prototype is freely distributable under the terms of an MIT-style license.
For details, see the Prototype web site: http://www.prototypejs.org/

Software - script.aculo.us

Script.aculo.us website

NOTE: Only the effects.js and dragdrop.js modules from Script.aculo.us are being used.

// script.aculo.us scriptaculous.js v1.9.0, Thu Dec 23 16:54:48 -0500 2010

// Copyright (c) 2005-2010 Thomas Fuchs (http://script.aculo.us, http://mir.aculo.us)
//
// Permission is hereby granted, free of charge, to any person obtaining
// a copy of this software and associated documentation files (the
// "Software"), to deal in the Software without restriction, including
// without limitation the rights to use, copy, modify, merge, publish,
// distribute, sublicense, and/or sell copies of the Software, and to
// permit persons to whom the Software is furnished to do so, subject to
// the following conditions:
//
// The above copyright notice and this permission notice shall be
// included in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
// LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
// OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
// WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
//
// For details, see the script.aculo.us web site: http://script.aculo.us/

Software - canvasXpress

canvasXpress website

CanvasXpress is a javascript library based on the <canvas> tag implemented in HTML5.

This package is currently being used for the Venn Diagram within SetBuilder. Plans are to utilize it in other areas in the generation of other graphs.

Software - Oracle Enterprise Edition

Oracle website

The data within Gataca is being stored in an Oracle 11g database.

Software - Modernizr

modernizr

modernizr provides simple interfacing to check to see what features are available within the client's browser. This is predomantly used to test for HTML 5 features such as canvas or local storage support.

Software - JQTouch

JQTouch website

JQTouch is being used for the mobile edition of Gataca.

Software - jQuery

JQuery website

jQuery is used within JQTouch only.

Software - tablesort

tablesort website

Copyright (c) 2006 Andrew Tetlaw 
http://tetlaw.id.au/view/blog/table-sorting-with-prototype/

Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use, copy,
modify, merge, publish, distribute, sublicense, and/or sell copies
of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.

Software - Firebug Light

Firebug Light website

firebugx.js - There is no disclaimer in the original file, but it is an open source project. The main website is http://www.getfirebug.com It is an open source project hosted by Google code.

Link-It Detail - Disease - Protein C Deficiency

Debug Stats

### Total Build Time: 22 ms 28.435 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 338 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 356 bytes
Skipping details on: CONCEPT_SYNONYM gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
Skipping details on: CONCEPT_TEXT gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_SEMANTIC_TYPE gt=1 ms Completed: 1 ms rowSize= 188 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=5 ms Completed: 5 ms rowSize= 1.413 KB
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=3 ms Completed: 3 ms rowSize= 5.430 KB
CONCEPT_RELATIONSHIPS gt=5 ms Completed: 5 ms rowSize= 10.782 KB
CONCEPT_GENES gt=4 ms Completed: 4 ms rowSize= 8.759 KB
CONCEPT_XREFS gt=0 Completed: 0 ms rowSize= 1.154 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Protein C Deficiency C0398625

Definition (1)

An absence or deficiency in PROTEIN C which leads to impaired regulation of blood coagulation. It is associated with an increased risk of severe or premature thrombosis. (Stedman's Med. Dict., 26th ed.)

Semantic Types (1)

Disease or Syndrome (T047)

Parents (3)

C0398623

C0005830

C0852077

Ancestral Roots

Relationships (23)

Relation Types:

diso_to_anat : 5

diso_to_chem : 3

diso_to_diso : 12

diso_to_phen : 2

diso_to_phys : 1

Relationships:

none : 16

is_associated_anatomic_site_of : 1

is_normal_cell_origin_of_disease : 1

is_normal_tissue_origin_of_disease : 1

isa : 2

mapped_to : 1

permuted_term_of : 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	70		Complication Aspects C1171258
DISO_to_DISO	69		Complication Aspects C1171258
DISO_to_PHEN	50		genetic aspects C0017399
DISO_to_PHEN	39		genetic aspects C0017399
DISO_to_CHEM	37		Protein C C0033621
DISO_to_CHEM	33		Protein C C0033621
DISO_to_DISO	29		DEFIC PROTEIN S C0242666
DISO_to_DISO	26		DEFIC PROTEIN S C0242666
DISO_to_DISO	26		Venous Thrombosis C0042487
DISO_to_ANAT	22		In Blood C0005768
DISO_to_DISO	20		Venous Thrombosis C0042487
DISO_to_ANAT	18		In Blood C0005768
DISO_to_DISO	16		Thrombosis C0040053
DISO_to_PHYS	16		Mutation C0026882
DISO_to_CHEM	12		Anticoagulants C0003280
DISO_to_DISO	12		Thrombosis C0040053
DISO_to_ANAT		is_normal_tissue_origin_of_disease	HEMOLYMPHORETICULAR TISSUE C1512398
DISO_to_ANAT		is_associated_anatomic_site_of	Hematopoietic and Lymphatic System C1512394
DISO_to_ANAT		is_normal_cell_origin_of_disease	Hematopoietic and Lymphoid Cell C1512385
DISO_to_DISO		mapped_to	Congenital thrombotic disease, due to Protein C deficiency C2930896
DISO_to_DISO		permuted_term_of	DEFIC PROTEIN C C0398625
DISO_to_DISO		isa	Hereditary protein C deficiency C0598221
DISO_to_DISO		isa	Thrombophilia due to acquired protein C deficiency C2585386

Genes (4)

Species:

human : 4

Species	Gene	GeneId	Gene Name	Evidence
Human	DPM1	8813	dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit	OMIM, Score=1000, UMLKSK CUI: C0398625 Protein C deficiency
Human	PROS1	5627	protein S (alpha)	GENERIF, Score=1000, Pubmed Id: 18824642, UMLKSK CUI: C0398625 Compared with nondeficient family members, subjects with protein S or protein C deficiency but not antithrombin deficiency have a higher risk for arterial thromboembolism before 55 years of age that is independent of prior venous thromboembolism
Human	PROC	5624	protein C (inactivator of coagulation factors Va and VIIIa)	GENERIF, Score=717, Pubmed Id: 12482406, UMLKSK CUI: C0398625 Smoking-induced vascular endothelium injury reduces activated protein C in a cigarette smoke dose-dependent manner, leading to activated protein C deficiency hypercoagulability OMIM, Score=909, UMLKSK CUI: C0398625 Acquired protein C deficiency seen in liver disease, DIC, and following surgery GENERIF, Score=1000, Pubmed Id: 18824642, UMLKSK CUI: C0398625 Compared with nondeficient family members, subjects with protein S or protein C deficiency but not antithrombin deficiency have a higher risk for arterial thromboembolism before 55 years of age that is independent of prior venous thromboembolism OMIM, Score=1000, UMLKSK CUI: C0398625 Protein C deficiency is found in 3-4% of patients with venous thromboembolism GENERIF, Score=1000, Pubmed Id: 15114590, UMLKSK CUI: C0398625 R147W mutation is a significant thrombotic risk factor and is the most common defect of PROC gene in Taiwanese patients with protein C deficiency GENERIF, Score=884, Pubmed Id: 18376272, UMLKSK CUI: C0398625 analysis of the protein C gene coding sequences in two sisters with severe congenital protein C deficiency identified 2 mutations in both patients, the previously described Arg169 to Trp mutation, and a novel mutation that changes Cys17 into a stop codon GENERIF, Score=1000, Pubmed Id: 16113807, UMLKSK CUI: C0398625 case report of a type I/II compound heterozygote newborn with protein C deficiency
Human	PAFAH1B2	5049	platelet-activating factor acetylhydrolase 1b, catalytic subunit 2 (30kDa)	GENERIF, Score=1000, Pubmed Id: 17849047, UMLKSK CUI: C0398625 PAFAH1B2 is not the gene responsible for the linkage evidence on chromosome 11q23 in protein C deficiency

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0398625	Protein C Deficiency	0		self

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