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 - Bronchopulmonary Dysplasia

Debug Stats

### Total Build Time: 78 ms 44.038 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 350 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 591 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= 1,011 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=6 ms Completed: 6 ms rowSize= 4.124 KB
CONCEPT_RELATIONSHIPS gt=37 ms Completed: 37 ms rowSize= 12.896 KB
CONCEPT_GENES gt=23 ms Completed: 23 ms rowSize= 23.733 KB
CONCEPT_XREFS gt=2 ms Completed: 2 ms rowSize= 1.160 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Bronchopulmonary Dysplasia C0006287

Definition (1)

A chronic lung disease developed after OXYGEN INHALATION THERAPY or mechanical ventilation (VENTILATION, MECHANICAL) usually occurring in certain premature infants (INFANT, PREMATURE) or newborn infants with respiratory distress syndrome (RESPIRATORY DISTRESS SYNDROME, NEWBORN). Histologically, it is characterized by the unusual abnormalities of the bronchioles, such as METAPLASIA, decrease in alveolar number, and formation of CYSTS.

Semantic Types (1)

Disease or Syndrome (T047)

Parents (2)

C0021295

C2350350

Ancestral Roots

Root	Root Plus One	Depth	Parent
Congenital, Hereditary, and Neonatal Diseases and Abnormalities C0027612	Infant, Newborn, Diseases C0021290	4	Infant, Premature, Diseases C0021295
Wounds and Injuries C0043251	Thoracic Injuries C0039980	5	Ventilator-Induced Lung Injury C2350350
Respiratory Tract Diseases C0035242	Lung Diseases C0024115	5	Ventilator-Induced Lung Injury C2350350

Relationships (71)

Relation Types:

diso_to_anat : 10

diso_to_chem : 40

diso_to_diso : 19

diso_to_phen : 2

Relationships:

none : 38

is_associated_anatomic_site_of : 3

isa : 1

may_prevent : 28

permuted_term_of : 1

Page Size

Current 25

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Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	60		Complication Aspects C1171258
DISO_to_DISO	56		INFANT VLBW C0282667
DISO_to_ANAT	55		Lung C0024109
DISO_to_DISO	50		Respiratory Distress Syndrome, Newborn C0035220
DISO_to_DISO	45		INFANT PREMATURE DIS C0021295
DISO_to_DISO	45		INFANT VLBW C0282667
DISO_to_DISO	42		Respiratory Distress Syndrome, Newborn C0035220
DISO_to_PHEN	36		genetic aspects C0017399
DISO_to_ANAT	34		Lung C0024109
DISO_to_DISO	34		Complication Aspects C1171258
DISO_to_DISO	29		INFANT PREMATURE DIS C0021295
DISO_to_PHEN	26		genetic aspects C0017399
DISO_to_DISO	25		HYPEROXIA C0242706
DISO_to_ANAT	24		In Blood C0005768
DISO_to_DISO	24		ELBW - Extremely low birth weight infant C0456065
DISO_to_CHEM	23		GLUCOCORTICOIDS C0017710
DISO_to_CHEM	21		Pulmonary Surfactants C0034085
DISO_to_CHEM	20		Nitric Oxide C0028128
DISO_to_ANAT	19		In Blood C0005768
DISO_to_CHEM	19		Dexamethasone C0011777
DISO_to_DISO	17		Chorioamnionitis C0008495
DISO_to_ANAT	16		Pulmonary Alveoli C0034051
DISO_to_DISO	16		Hypertension, Pulmonary C0020542
DISO_to_CHEM	15		Anti-Inflammatory Agents C0003209
DISO_to_CHEM	15		Dexamethasone C0011777

Genes (19)

Species:

human : 19

Species	Gene	GeneId	Gene Name	Evidence
Human	SFTPA1	653509	surfactant protein A1	GAD, Score=1000, Pubmed Id: 15102713, UMLKSK CUI: C0006287 Title:Data mining and multiparameter analysis of lung surfactant protein genes in bronchopulmonary dysplasia\|Association:Not Found\|Conclusion:We propose that two separate SP-B gene polymorphisms have a phenotypic significance via
Human	TIMP2	7077	TIMP metallopeptidase inhibitor 2	GENERIF, Score=1000, Pubmed Id: 14973177, UMLKSK CUI: C0006287 MMP and TIMP may be involved in the feto-neonatal development and may contribute to the pathogenesis of bronchopulmonary dysplasia and/or intraventricular hemorrhage in critically ill preterm neonates
Human	TIMP1	7076	TIMP metallopeptidase inhibitor 1	GENERIF, Score=1000, Pubmed Id: 14973177, UMLKSK CUI: C0006287 MMP and TIMP may be involved in the feto-neonatal development and may contribute to the pathogenesis of bronchopulmonary dysplasia and/or intraventricular hemorrhage in critically ill preterm neonates GENERIF, Score=734, Pubmed Id: 12376362, UMLKSK CUI: C0006287 MMP-9 level and TIMP-1 levels increased after birth but are not linked to bronchopulmonary dysplasia outcome; low MMP-2 level at birth is associated with the development of BPD
Human	SFTPD	6441	surfactant protein D	GAD, Score=1000, Pubmed Id: 15102713, UMLKSK CUI: C0006287 Title:Data mining and multiparameter analysis of lung surfactant protein genes in bronchopulmonary dysplasia\|Association:Not Found\|Conclusion:We propose that two separate SP-B gene polymorphisms have a phenotypic significance via
Human	SFTPC	6440	surfactant protein C	GAD, Score=1000, Pubmed Id: 15102713, UMLKSK CUI: C0006287 Title:Data mining and multiparameter analysis of lung surfactant protein genes in bronchopulmonary dysplasia\|Association:Not Found\|Conclusion:We propose that two separate SP-B gene polymorphisms have a phenotypic significance via
Human	SFTPB	6439	surfactant protein B	GAD, Score=1000, Pubmed Id: 15102713, UMLKSK CUI: C0006287 Title:Data mining and multiparameter analysis of lung surfactant protein genes in bronchopulmonary dysplasia\|Association:Not Found\|Conclusion:We propose that two separate SP-B gene polymorphisms have a phenotypic significance via
Human	SFTPA2B	6436		GAD, Score=1000, Pubmed Id: 11105614, UMLKSK CUI: C0006287 Title:Polymorphisms of surfactant protein A genes and the risk of bronchopulmonary dysplasia in preterm infants\|Association:Not Found\|Conclusion:In addition to previously established risk factors for BPD, 6A6 polymorphism for SP-A1 gene is an independent co-factor. We believe treatment of neonatal RDS should also include stratification according to genetic risk factors.
Human	PRSS2	5645	protease, serine, 2 (trypsin 2)	GENERIF, Score=1000, Pubmed Id: 12949286, UMLKSK CUI: C0006287 High levels of pulmonary trypsin-2 may be associated with the development of bronchopulmonary dysplasia in preterm infants
Human	MMP16	4325	matrix metallopeptidase 16 (membrane-inserted)	GENERIF, Score=1000, Pubmed Id: 18784838, UMLKSK CUI: C0006287 MMP16 polymorphisms appear to influence not only the pulmonary expression and function of MMP16 but also the risk of bronchopulmonary dysplasia
Human	MMP9	4318	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	GENERIF, Score=734, Pubmed Id: 12376362, UMLKSK CUI: C0006287 MMP-9 level and TIMP-1 levels increased after birth but are not linked to bronchopulmonary dysplasia outcome; low MMP-2 level at birth is associated with the development of BPD GENERIF, Score=1000, Pubmed Id: 14973177, UMLKSK CUI: C0006287 MMP and TIMP may be involved in the feto-neonatal development and may contribute to the pathogenesis of bronchopulmonary dysplasia and/or intraventricular hemorrhage in critically ill preterm neonates
Human	MMP2	4313	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	GENERIF, Score=1000, Pubmed Id: 14973177, UMLKSK CUI: C0006287 MMP and TIMP may be involved in the feto-neonatal development and may contribute to the pathogenesis of bronchopulmonary dysplasia and/or intraventricular hemorrhage in critically ill preterm neonates GENERIF, Score=734, Pubmed Id: 12376362, UMLKSK CUI: C0006287 MMP-9 level and TIMP-1 levels increased after birth but are not linked to bronchopulmonary dysplasia outcome; low MMP-2 level at birth is associated with the development of BPD
Human	IL10	3586	interleukin 10	GENERIF, Score=1000, Pubmed Id: 17237722, UMLKSK CUI: C0006287 constitutive expression of IL-10 by lung inflammatory cells is associated with the risk for bronchopulmonary dysplasia
Human	IL1RN	3557	interleukin 1 receptor antagonist	GENERIF, Score=1000, Pubmed Id: 15539764, UMLKSK CUI: C0006287 strong and early expression of interleukin-1 receptor antagonist(IL-1Ra) proves to be non-protective due to the robust expression of airway agonist interleukin-1beta seen by day 5 in premature infants who develop bronchopulmonary dysplasia (BPD)
Human	IL1B	3553	interleukin 1, beta	GENERIF, Score=1000, Pubmed Id: 15539764, UMLKSK CUI: C0006287 strong and early expression of interleukin-1 receptor antagonist(IL-1Ra) proves to be non-protective due to the robust expression of airway agonist interleukin-1beta seen by day 5 in premature infants who develop bronchopulmonary dysplasia (BPD)
Human	TNC	3371	tenascin C	GENERIF, Score=1000, Pubmed Id: 11850444, UMLKSK CUI: C0006287 tenascin-C is highly expressed in the walls of alveoli and bronchioli in respiratory distress syndrome and bronchopulmonary dysplasia
Human	GSTA6P	2942	glutathione S-transferase alpha 6, pseudogene	GENERIF, Score=1000, Pubmed Id: 14726935, UMLKSK CUI: C0006287 The polymorphism of DSTAP1 are associated with the development of bronchopulmonary dysplasia
Human	FGF7	2252	fibroblast growth factor 7	GENERIF, Score=1000, Pubmed Id: 12016100, UMLKSK CUI: C0006287 KGF may hold promise for the treatment of very premature neonates with bronchopulmonary dysplasia
Human	F2RL1	2150	coagulation factor II (thrombin) receptor-like 1	GENERIF, Score=1000, Pubmed Id: 15879299, UMLKSK CUI: C0006287 strong expression of PAR(2) was detected in myofibroblasts of thickened and fibrotic alveolar walls in prolonged respiratory distress syndrome or bronchopulmonary dysplasia
Human	ACE	1636	angiotensin I converting enzyme	GENERIF, Score=1000, Pubmed Id: 16356438, UMLKSK CUI: C0006287 The D allele of ACE is associated with an increased risk and severity of bronchopulmonary dysplasia

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0006287	Bronchopulmonary Dysplasia	0		self

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