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 - Pulmonary Embolism

Debug Stats

### Total Build Time: 696 ms 38.274 KB
CONCEPT_NAME gt=7 ms Completed: 7 ms rowSize= 334 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 1.168 KB
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=22 ms Completed: 22 ms rowSize= 975 bytes
CONCEPT_CHILDREN gt=6 ms Completed: 6 ms rowSize= 558 bytes
CONCEPT_ANCESTRAL_ROOTS gt=3 ms Completed: 3 ms rowSize= 2.762 KB
CONCEPT_RELATIONSHIPS gt=623 ms Completed: 623 ms rowSize= 15.260 KB
CONCEPT_GENES gt=27 ms Completed: 27 ms rowSize= 15.898 KB
CONCEPT_XREFS gt=5 ms Completed: 5 ms rowSize= 1.152 KB
CONCEPT_ANCILLARY gt=2 ms Completed: 2 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Pulmonary Embolism C0034065

Definition (1)

A pulmonary embolism is a sudden blockage in a lung artery. The cause is usually a blood clot in the leg called a deep vein thrombosis that breaks loose and travels through the bloodstream to the lung. Pulmonary embolism is a serious condition that can cause

Permanent damage to the affected lung
Low oxygen levels in your blood
Damage to other organs in your body from not getting enough oxygen

If a clot is large, or if there are many clots, pulmonary embolism can cause death.

Half the people who have pulmonary embolism have no symptoms. If you do have symptoms, they can include shortness of breath, chest pain or coughing up blood. Symptoms of a blood clot include warmth, swelling, pain, tenderness and redness of the leg. The goal of treatment is to break up clots and help keep other clots from forming.

NIH: National Heart, Lung, and Blood Institute

Semantic Types (1)

Disease or Syndrome (T047)

Parents (2)

C0013922

C0024115

Children (1)

C0034074

Ancestral Roots

Root	Root Plus One	Depth	Parent
Cardiovascular Diseases C0007222	Vascular Diseases C0042373	5	Embolism C0013922
Respiratory Tract Diseases C0035242	Lung Diseases C0024115	3	Lung Diseases C0024115

Relationships (270)

Relation Types:

diso_to_anat : 19

diso_to_chem : 149

diso_to_diso : 93

diso_to_phen : 2

diso_to_phys : 7

Relationships:

none : 118

associated_with : 1

entry_version_of : 1

is_associated_anatomic_site_of : 2

isa : 15

location_of : 1

mapped_to : 1

may_prevent : 54

may_treat : 71

parent_is_cdrh : 1

related_to : 4

used_for : 1

Page Size

Current 25

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Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	695		Venous Thrombosis C0042487
DISO_to_DISO	684		Venous Thrombosis C0042487
DISO_to_DISO	652		Complication Aspects C1171258
DISO_to_DISO	439		Complication Aspects C1171258
DISO_to_ANAT	298		In Blood C0005768
DISO_to_CHEM	272		Anticoagulants C0003280
DISO_to_DISO	241		Hypertension, Pulmonary C0020542
DISO_to_DISO	238		Venous Thromboembolism C1861172
DISO_to_ANAT	224		In Blood C0005768
DISO_to_ANAT	220		Pulmonary Artery C0034052
DISO_to_CHEM	198		Anticoagulants C0003280
DISO_to_DISO	166		Hypertension, Pulmonary C0020542
DISO_to_CHEM	157		Fibrinolytic Agents C0016018
DISO_to_DISO	154		COMPL POSTOP C0032787
DISO_to_DISO	132		COMPL POSTOP C0032787
DISO_to_DISO	132		Thrombosis C0040053
DISO_to_ANAT	131		Pulmonary Artery C0034052
DISO_to_CHEM	129		Fibrin Fibrinogen Degradation Products C0163275
DISO_to_CHEM	126		Fibrin Fibrinogen Degradation Products C0163275
DISO_to_CHEM	121		Fibrinolytic Agents C0016018
DISO_to_DISO	115		DYSFUNCTION, RIGHT VENTRICULAR C0242707
DISO_to_CHEM	82		Heparin C0019134
DISO_to_DISO	82		Thrombosis C0040053
DISO_to_ANAT	81		Lung C0024109
DISO_to_DISO	79		Thromboembolism C0040038

Genes (12)

Species:

human : 12

Species	Gene	GeneId	Gene Name	Evidence
Human	P2RY12	64805	purinergic receptor P2Y, G-protein coupled, 12	GENERIF, Score=1000, Pubmed Id: 17707382, UMLKSK CUI: C0034065 the haplotype H2 of purinergic receptor P2Y G-protein coupled 12 (P2RY12) was significantly associated with a lower risk of incident Deep vein thrombosis/pulmonary embolism as compared to the reference haplotype H1
Human	TNNI3	7137	troponin I type 3 (cardiac)	GENERIF, Score=901, Pubmed Id: 18094010, UMLKSK CUI: C0034065 in haemodynamically stable patients with acute pulmonary embolism, cardiac troponin I was not an independent predictor of 30-day all-cause mortality, although it did predict fatal pulmonary embolism
Human	PROS1	5627	protein S (alpha)	OMIM, Score=1000, UMLKSK CUI: C0034065 Pulmonary embolism
Human	PROC	5624	protein C (inactivator of coagulation factors Va and VIIIa)	GENERIF, Score=734, Pubmed Id: 18160601, UMLKSK CUI: C0034065 Protein C mutation incidence was higher in the pulmonary emboli group than in the deep vein thrombosis (8.33%) and cerebral vein thrombosis (16.1%) groups OMIM, Score=1000, UMLKSK CUI: C0034065 Pulmonary embolism
Human	PODXL	5420	podocalyxin-like	GENERIF, Score=901, Pubmed Id: 18818395, UMLKSK CUI: C0034065 PODXL(hi)/CD49f(hi) MSCs were less prone to produce lethal pulmonary emboli
Human	SERPINF2	5345	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2	GENERIF, Score=901, Pubmed Id: 12911586, UMLKSK CUI: C0034065 Alpha2-antiplasmin has an important role in acute pulmonary embolism
Human	ITGA6	3655	integrin, alpha 6	GENERIF, Score=901, Pubmed Id: 18818395, UMLKSK CUI: C0034065 PODXL(hi)/CD49f(hi) MSCs were less prone to produce lethal pulmonary emboli
Human	F13A1	2162	coagulation factor XIII, A1 polypeptide	GENERIF, Score=1000, Pubmed Id: 12958612, UMLKSK CUI: C0034065 direct relation of FXIII A-subunit to fibrinogen levels argues for significant consumption of these coagulation factors in pulmonary embolism GENERIF, Score=1000, Pubmed Id: 12958613, UMLKSK CUI: C0034065 investigate the hypothesisis that TAFI -438 G/A and factor XIIIA Val34Leu polymorphisms might influence the formation and fate of emboli and accordingly the risk of pulmonary embolism in a case control study
Human	F5	2153	coagulation factor V (proaccelerin, labile factor)	GENERIF, Score=1000, Pubmed Id: 11806843, UMLKSK CUI: C0034065 This review of hemostatic variables identifying those at risk of in-patient hospital death from pulmonary embolism (PE)notes that the prevalence of factor V Leiden may be a 'milder' genetic risk factor for PE than for deep venous thrombosis GENERIF, Score=1000, Pubmed Id: 18617648, UMLKSK CUI: C0034065 Examine possible mechanisms for fact that factor V Leiden mutation carriers have an substantially increased risk of deep venous thrombosis, whereas the risk of pulmonary embolism (PE) is only mildly increased
Human	CRP	1401	C-reactive protein, pentraxin-related	GENERIF, Score=901, Pubmed Id: 17456635, UMLKSK CUI: C0034065 evaluate the role of acute phase of inflammation in the elderly patients with suspected and confirmed pulmonary embolism
Human	CPB2	1361	carboxypeptidase B2 (plasma)	GENERIF, Score=1000, Pubmed Id: 12871455, UMLKSK CUI: C0034065 Plasma levels of TAFI were not elevated in pulmonary embolism, except in cases with a high clot burden, suggesting that TAFI levels might be secondarily increased by release from activated platelets GENERIF, Score=1000, Pubmed Id: 12958613, UMLKSK CUI: C0034065 investigate the hypothesisis that TAFI -438 G/A and factor XIIIA Val34Leu polymorphisms might influence the formation and fate of emboli and accordingly the risk of pulmonary embolism in a case control study
Human	ALB	213	albumin	GENERIF, Score=734, Pubmed Id: 18513410, UMLKSK CUI: C0034065 Ischemia-modified albumin is a good alternative to D-dimer in pulmonary embolism diagnosis in terms of both cost and efficiency

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0034065	Pulmonary Embolism	0		self

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