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 - Rickets

Debug Stats

### Total Build Time: 50 ms 43.707 KB
CONCEPT_NAME gt=3 ms Completed: 3 ms rowSize= 312 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 196 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= 244 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=3 ms Completed: 3 ms rowSize= 1.411 KB
CONCEPT_CHILDREN gt=2 ms Completed: 2 ms rowSize= 1,019 bytes
CONCEPT_ANCESTRAL_ROOTS gt=3 ms Completed: 3 ms rowSize= 4.089 KB
CONCEPT_RELATIONSHIPS gt=27 ms Completed: 27 ms rowSize= 14.146 KB
CONCEPT_GENES gt=10 ms Completed: 10 ms rowSize= 21.162 KB
CONCEPT_XREFS gt=1 ms Completed: 1 ms rowSize= 1.142 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (1)

Rickets C0035579

Definition (1)

a condition caused by vitamin D deficiency

Semantic Types (2)

Disease or Syndrome (T047)

Injury or Poisoning (T037)

Parents (3)

C0006705

C0042870

C0005944

Children (2)

C0733682

C0035086

Ancestral Roots

Root	Root Plus One	Depth	Parent
Nutritional and Metabolic Diseases C0028715	Metabolic Diseases C0025517	4	Calcium Metabolism Disorders C0006705
Nutritional and Metabolic Diseases C0028715	Nutrition Disorders C0028709	7	Vitamin D Deficiency C0042870
Musculoskeletal Diseases C0026857	Bone Diseases C0005940	4	Bone Diseases, Metabolic C0005944

Relationships (56)

Relation Types:

diso_to_anat : 4

diso_to_chem : 21

diso_to_diso : 23

diso_to_gene : 6

diso_to_phen : 2

Relationships:

none : 15

clinically_similar : 1

gene_associated_with_disease : 6

is_normal_tissue_origin_of_disease : 1

is_primary_anatomic_site_of_disease : 1

isa : 14

mapped_to : 1

may_treat : 14

related_to : 3

Page Size

Current 25

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Prior Page

Current 1

Relation Type	Co-Occuring Concept Count	Relationship	Concept
DISO_to_DISO	69		AVITAMINOSIS D C0042870
DISO_to_CHEM	52		Vitamin D C0042866
DISO_to_CHEM	49		Vitamin D C0042866
DISO_to_DISO	47		Complication Aspects C1171258
DISO_to_DISO	45		AVITAMINOSIS D C0042870
DISO_to_PHEN	41		genetic aspects C0017399
DISO_to_PHEN	40		genetic aspects C0017399
DISO_to_DISO	36		Complication Aspects C1171258
DISO_to_ANAT	23		In Blood C0005768
DISO_to_DISO	17		Osteomalacia C0029442
DISO_to_CHEM	15		Receptors, Calcitriol C0108082
DISO_to_CHEM	14		Calcium C0006675
DISO_to_CHEM	14		Receptors, Calcitriol C0108082
DISO_to_ANAT	13		In Blood C0005768
DISO_to_CHEM	12		Calcium C0006675
DISO_to_ANAT		is_normal_tissue_origin_of_disease	Connective and Soft Tissue C1516798
DISO_to_ANAT		is_primary_anatomic_site_of_disease	Skeletal bone C0262950
DISO_to_CHEM		may_treat	CALCITRIOL 0.2 GM ORAL CAPSULE, LIQUID FILLED C0975120
DISO_to_CHEM		may_treat	CALCITRIOL 0.5 MCG ORAL CAPSULE C0975121
DISO_to_CHEM		may_treat	CALCITRIOL 1 MCG INTRAVENOUS INJECTION C0975122
DISO_to_CHEM		may_treat	CALCITRIOL 1 MCG ORAL LIQUID C0981370
DISO_to_CHEM		may_treat	CALCITRIOL 2 MCG INJECTION, SOLUTION C0975123
DISO_to_CHEM		may_treat	CALCITRIOL 3 mcg/gram TOPICAL OINTMENT(GM) C1273274
DISO_to_CHEM		may_treat	Calciferol 1.25mg tablet C0976697
DISO_to_CHEM		may_treat	Calciferol, 500000 iu/ml injectable solution C0976696

Genes (16)

Species:

human : 16

Species	Gene	GeneId	Gene Name	Evidence
Human	SLC34A3	142680	solute carrier family 34 (type II sodium/phosphate contransporter), member 3	OMIM, Score=1000, UMLKSK CUI: C0035579 Heterozygotes have milder metabolic defect with increased serum 1,25(OH)2D3 and hypercalciuria, but no bone disease or rickets OMIM, Score=1000, UMLKSK CUI: C0035579 Rickets
Human	CYP2R1	120227	cytochrome P450, family 2, subfamily R, polypeptide 1	OMIM, Score=1000, UMLKSK CUI: C0035579 Rickets GENERIF, Score=861, Pubmed Id: 18511070, UMLKSK CUI: C0035579 The structure reveals the secosteroid binding mode in an extended active site and allows rationalization of the molecular basis of the inherited rickets associated with CYP2R1
Human	FGF23	8074	fibroblast growth factor 23	OMIM, Score=1000, UMLKSK CUI: C0035579 Rickets (childhood-onset)
Human	VDR	7421	vitamin D (1,25- dihydroxyvitamin D3) receptor	GENERIF, Score=812, Pubmed Id: 18365588, UMLKSK CUI: C0035579 Our results indicated that VDR gene polymorphisms might be an important factor for genetic susceptibility to vitamin D deficient rickets in the Turkish population GENERIF, Score=804, Pubmed Id: 12468277, UMLKSK CUI: C0035579 Novel mutation in the VDR, Q317X, is the molecular defect in a patient with 1,25-dihydroxyvitamin D resistant rickets GENERIF, Score=804, Pubmed Id: 12403843, UMLKSK CUI: C0035579 A novel mutation in helix 12 of this receptor impairs coactivator interaction and causes hereditary 1,25-dihydroxyvitamin D-resistant rickets without alopecia GENERIF, Score=1000, Pubmed Id: 17551469, UMLKSK CUI: C0035579 Polymorphisms in the Vitamin D receptor (VDR) gene were postulated to be associated with bone mineral density; VDR gene polymorphism could be influential in the development of rickets in some children as well [review] GAD, Score=1000, Pubmed Id: 14746673, UMLKSK CUI: C0035579 Title:[Association of the vitamin D receptor gene start codon polymorphism with vitamin D deficiency rickets]\|Association:Y\|Conclusion:There is an association between VDR gene start codon polymorphism and vitamin D deficiency rickets. This study suggested the possibility that VDR gene polymorphism might be important in determining an individual's susceptibility to development of vitamin D deficiency rickets. OMIM, Score=1000, UMLKSK CUI: C0035579 Rickets GENERIF, Score=812, Pubmed Id: 14746673, UMLKSK CUI: C0035579 Result suggested the possibility that vitamin D receptor gene polymorphism might be important in determining an individual's susceptibility to development of vitamin D deficiency rickets
Human	TALDO1	6888	transaldolase 1	GENERIF, Score=1000, Pubmed Id: 18331807, UMLKSK CUI: C0035579 A new case of TALDO deficiency resulted in cirrhosis, rickets and deafness
Human	PRL	5617	prolactin	GENERIF, Score=1000, Pubmed Id: 17785327, UMLKSK CUI: C0035579 Hyperprolactinemia, hyperferritinemia, and hypovitaminosis D have different immunological implications in the pathogenesis of the autoimmune diseases
Human	PHEX	5251	phosphate regulating endopeptidase homolog, X-linked	OMIM, Score=1000, UMLKSK CUI: C0035579 Rickets in children
Human	OCRL	4952	oculocerebrorenal syndrome of Lowe	OMIM, Score=1000, UMLKSK CUI: C0035579 Rickets (in approximately 33% of patients)
Human	HLA-DQB1	3119		OMIM, Score=1000, UMLKSK CUI: C0035579 Presentation in children - diarrhea, constipation (rarely), short stature, pubertal delay, rickets, iron and folate deficiency with anemia
Human	HLA-DQA1	3117		OMIM, Score=1000, UMLKSK CUI: C0035579 Presentation in children - diarrhea, constipation (rarely), short stature, pubertal delay, rickets, iron and folate deficiency with anemia
Human	CYP27B1	1594	cytochrome P450, family 27, subfamily B, polypeptide 1	OMIM, Score=1000, UMLKSK CUI: C0035579 Rickets
Human	CTNS	1497	cystinosin, lysosomal cystine transporter	OMIM, Score=1000, UMLKSK CUI: C0035579 Rickets
Human	COL2A1	1280	collagen, type II, alpha 1	OMIM, Score=777, UMLKSK CUI: C0035579 Irregular, rachitic-like metaphyses
Human	CLCN5	1184	chloride channel, voltage-sensitive 5	OMIM, Score=1000, UMLKSK CUI: C0035579 Rickets OMIM, Score=1000, UMLKSK CUI: C0035579 Rickets (in approximately 33% of patients)
Human	ALPL	249	alkaline phosphatase, liver/bone/kidney	OMIM, Score=1000, UMLKSK CUI: C0035579 Rickets (hypophosphatasia only) OMIM, Score=1000, UMLKSK CUI: C0035579 Rickets and premature primary tooth loss occur in childhood
Human	ACP5	54	acid phosphatase 5, tartrate resistant	INFERRED, Score=800, UMLKSK CUI: C0035579

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0035579	Rickets	0		self

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