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 - Epidermolysis Bullosa Dystrophica

Debug Stats

### Total Build Time: 25 ms 32.596 KB
CONCEPT_NAME gt=4 ms Completed: 4 ms rowSize= 428 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 528 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=0 Completed: 0 ms rowSize= 188 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=2 ms Completed: 2 ms rowSize= 992 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=5 ms Completed: 5 ms rowSize= 5.449 KB
CONCEPT_RELATIONSHIPS gt=8 ms Completed: 8 ms rowSize= 13.695 KB
CONCEPT_GENES gt=4 ms Completed: 4 ms rowSize= 10.163 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.167 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (2)

Epidermolysis Bullosa Dystrophica C0079294

Bullosa Dystrophica, Epidermolysis

Definition (1)

Form of epidermolysis bullosa characterized by atrophy of blistered areas, severe scarring, and nail changes. It is most often present at birth or in early infancy and occurs in both autosomal dominant and recessive forms. All forms of dystrophic epidermolysis bullosa result from mutations in COLLAGEN TYPE VII, a major component fibrils of BASEMENT MEMBRANE and EPIDERMIS.

Semantic Types (1)

Disease or Syndrome (T047)

Parents (2)

C0014527

C0009326

Ancestral Roots

Relationships (26)

Relation Types:

diso_to_anat : 4

diso_to_chem : 3

diso_to_diso : 13

diso_to_gene : 1

diso_to_phen : 2

diso_to_phys : 3

Relationships:

none : 17

is_associated_anatomic_site_of : 1

is_finding_of_disease : 1

is_primary_anatomic_site_of_disease : 1

isa : 2

mapped_to : 3

permuted_term_of : 1

Page Size

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Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_PHEN	111		genetic aspects C0017399
DISO_to_CHEM	75		Collagen Type VII C0009337
DISO_to_PHEN	73		genetic aspects C0017399
DISO_to_DISO	60		Complication Aspects C1171258
DISO_to_DISO	51		Complication Aspects C1171258
DISO_to_CHEM	43		Collagen Type VII C0009337
DISO_to_PHYS	28		Mutation C0026882
DISO_to_DISO	17		Carcinoma, Squamous Cell C0007137
DISO_to_DISO	17		Cutaneous tumor C0037286
DISO_to_DISO	16		Carcinoma, Squamous Cell C0007137
DISO_to_PHYS	16		Mutation C0026882
DISO_to_ANAT	13		Skin C1123023
DISO_to_PHYS	10		Missense Mutation C0599155
DISO_to_ANAT	8		Fibroblasts C0016030
DISO_to_CHEM	8		Collagen C0009325
DISO_to_DISO	8		Esophageal Stenosis C0014866
DISO_to_GENE	8		Gene, Recessive C0017361
DISO_to_ANAT		is_associated_anatomic_site_of	Integumentary System C0037267
DISO_to_ANAT		is_primary_anatomic_site_of_disease	Skin C1123023
DISO_to_DISO		permuted_term_of	Bullosa Dystrophica, Epidermolysis C0079294
DISO_to_DISO		is_finding_of_disease	Cutaneous Involvement C1511567
DISO_to_DISO		mapped_to	DEB, PRETIBIAL C0432321
DISO_to_DISO		mapped_to	DYSTROPHIC EPIDERMOLYSIS BULLOSA, NEONATAL C1851573
DISO_to_DISO		mapped_to	Dominant dystrophic epidermolysis bullosa, albopapular type (disorder) C0432322
DISO_to_DISO		isa	Generalised dystrophic epidermolysis bullosa C0474887

Genes (2)

Species:

human : 2

Species	Gene	GeneId	Gene Name	Evidence
Human	COL7A1	1294	collagen, type VII, alpha 1	GENERIF, Score=756, Pubmed Id: 18440202, UMLKSK CUI: C0079294 A p.Glu2857X mutation exhibits mild pathogenic effects in COL7A1, and its uniqueness enables detailed analysis and comparison of the destabilizing effects of missense mutations in dystrophic epidermolysis bullosa patients GAD, Score=1000, Pubmed Id: 12485454, UMLKSK CUI: C0079294 Title:Genotype-phenotype correlation in italian patients with dystrophic epidermolysis bullosa.\|Association:Not Found\|Conclusion:Indeed, haplotype analysis supported propagation of ancestral mutated alleles within the Italian population for these particular mutations. Altogether recurrent mutations account for approximately 43% of RDEB alleles in Italian patients and therefore new DEB patients should first be screened for the presence of these mutations. GENERIF, Score=1000, Pubmed Id: 17425959, UMLKSK CUI: C0079294 We report 14 Australian families with different forms of dystrophic epidermolysis bullosa (DEB) with 23 different COL7A1 allelic variants, nine of which were novel OMIM, Score=1000, UMLKSK CUI: C0079294 Dystrophic epidermolysis bullosa GENERIF, Score=1000, Pubmed Id: 18450758, UMLKSK CUI: C0079294 known recessive DEB C7 mutations perturb critical functions of the C7 molecule and may have a role in dystrophic epidermolysis bullosa GENERIF, Score=1000, Pubmed Id: 18429782, UMLKSK CUI: C0079294 Mutations in the gene for collagen VII (COL7A1) have been documented in both types of dystrophic epidermolysis bullosa GAD, Score=1000, Pubmed Id: 15888141, UMLKSK CUI: C0079294 Title:High frequency of the 425A-->G splice-site mutation and novel mutations of the COL7A1 gene in central Europe: significance for future mutation detectionstrategies in dystrophic epidermolysis bullosa.\|Association:Not Found\|Conclusion:High recurrence of the splice-site mutation 425A-->G in central European patients with DEB should be taken into account when designing COL7A1 mutation detection strategies. Reporting of three novel COL7A1 mutations in this study further emphasizes the molecular heterogeneity of DEB and provides more information for studies on genotype-phenotype correlations in different DEB subtypes. GENERIF, Score=1000, Pubmed Id: 16923137, UMLKSK CUI: C0079294 Two boys with dystrophic epidermolysis bullosa and their fathers revealed a heterozygous nucleotide G to A transition at position 6109 and 6082 in 73 exon of COL7A1, which resulted in a glycine to arginine substitution (G2037R and G2028R), respectively GENERIF, Score=756, Pubmed Id: 18558993, UMLKSK CUI: C0079294 characterization of COL7A1 mutations in dystrophic epidermolysis bullosa [review] GENERIF, Score=1000, Pubmed Id: 15816848, UMLKSK CUI: C0079294 Spectrum of mutations in dystrophic epidermolysis bullosa and cryptic splicing GENERIF, Score=1000, Pubmed Id: 18496702, UMLKSK CUI: C0079294 linked to dystrophic epidermolysis bullosa in Tunisian consanguineous families
Human	COL1A1	1277	collagen, type I, alpha 1	GENERIF, Score=1000, Pubmed Id: 12787275, UMLKSK CUI: C0079294 COL7A1 mutation is characteristic in patients with dystrophic epidermolysis bullosa

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0079294	Epidermolysis Bullosa Dystrophica	0		self

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