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 - Osteopetrosis

Debug Stats

### Total Build Time: 69 ms 32.446 KB
CONCEPT_NAME gt=0 Completed: 0 ms rowSize= 378 bytes
CONCEPT_SOLR_HIT_STATS gt=0 Completed: 0 ms rowSize= 14 bytes
CONCEPT_DEFINITION gt=0 Completed: 0 ms rowSize= 342 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= 247 bytes
Skipping details on: CONCEPT_NAMESPACE gt=NONE 0 Completed: 0 ms rowSize= 0 bytes
CONCEPT_PARENTS gt=3 ms Completed: 3 ms rowSize= 550 bytes
CONCEPT_CHILDREN gt=0 Completed: 0 ms rowSize= 8 bytes
CONCEPT_ANCESTRAL_ROOTS gt=0 Completed: 0 ms rowSize= 1.499 KB
CONCEPT_RELATIONSHIPS gt=58 ms Completed: 58 ms rowSize= 13.900 KB
CONCEPT_GENES gt=7 ms Completed: 7 ms rowSize= 14.383 KB
CONCEPT_XREFS gt=0 Completed: 0 ms rowSize= 1.147 KB
CONCEPT_ANCILLARY gt=1 ms Completed: 1 ms rowSize= 14 bytes
Reload Stats

Disease (2)

Osteopetrosis C0029454

Albers-Schonberg disease

Definition (1)

Excessive formation of dense trabecular bone leading to pathological fractures; OSTEITIS; SPLENOMEGALY with infarct; ANEMIA; and extramedullary hemopoiesis (HEMATOPOIESIS, EXTRAMEDULLARY).

Semantic Types (2)

Disease or Syndrome (T047)

Congenital Abnormality (T019)

Parents (1)

C0029464

Ancestral Roots

Root	Root Plus One	Depth	Parent
Musculoskeletal Diseases C0026857	Bone Diseases C0005940	6	Osteosclerosis C0029464

Relationships (59)

Relation Types:

diso_to_anat : 7

diso_to_chem : 14

diso_to_diso : 32

diso_to_gene : 1

diso_to_phen : 2

diso_to_phys : 3

Relationships:

none : 30

classifies : 2

is_associated_anatomic_site_of : 1

is_primary_anatomic_site_of_disease : 1

isa : 4

mapped_to : 17

may_treat : 3

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_PHEN	92		genetic aspects C0017399
DISO_to_PHEN	83		genetic aspects C0017399
DISO_to_DISO	63		Complication Aspects C1171258
DISO_to_DISO	48		Complication Aspects C1171258
DISO_to_ANAT	25		Osteoclast C0029431
DISO_to_ANAT	24		Osteoclast C0029431
DISO_to_PHYS	15		Mutation C0026882
DISO_to_CHEM	13		Chloride Channels C0055363
DISO_to_DISO	13		Disease, Mandibular C0024689
DISO_to_DISO	13		Osteomyelitis C0029443
DISO_to_CHEM	12		Macrophage Colony-Stimulating Factor C0079784
DISO_to_ANAT	11		BONE BONES C0005931
DISO_to_CHEM	11		Vacuolar Proton-Translocating ATPases C0379099
DISO_to_CHEM	10		Chloride Channels C0055363
DISO_to_CHEM	8		Vacuolar Proton-Translocating ATPases C0379099
DISO_to_DISO	7		Acidosis, Renal Tubular C0001126
DISO_to_DISO	7		Osteomyelitis C0029443
DISO_to_ANAT	6		BONE BONES C0005931
DISO_to_CHEM	6		Macrophage Colony-Stimulating Factor C0079784
DISO_to_CHEM	6		RANK Ligand C0666364
DISO_to_ANAT	5		In Blood C0005768
DISO_to_CHEM	5		Carbonic Anhydrase II C0007034
DISO_to_CHEM	5		Diphosphonates C0012544
DISO_to_CHEM	5		Membrane Associated Proteins C0025252
DISO_to_CHEM	5		Receptor Activator of Nuclear Factor-kappa B C0961340

Genes (8)

Species:

human : 8

Species	Gene	GeneId	Gene Name	Evidence
Human	OSTM1	28962	osteopetrosis associated transmembrane protein 1	GENERIF, Score=827, Pubmed Id: 17985267, UMLKSK CUI: C0029454 This study reports on a 12-month-old female with recessive OSMT1 mutations and neuroimaging findings suggesting a malignant infantile osteopetrosis
Human	PLEKHM1	9842	pleckstrin homology domain containing, family M (with RUN domain) member 1	GENERIF, Score=694, Pubmed Id: 17997709, UMLKSK CUI: C0029454 heterozygous mutation (R714C) of the osteopetrosis gene, pleckstrin homolog domain containing family M (with run domain) member 1 (PLEKHM1), impairs vesicular acidification and increases TRACP secretion in osteoclasts GENERIF, Score=1000, Pubmed Id: 17404618, UMLKSK CUI: C0029454 PLEKHM1 is a novel gene implicated in the development of osteopetrosis, with a putative critical function in vesicular transport in the osteoclast
Human	TNFSF11	8600	tumor necrosis factor (ligand) superfamily, member 11	GENERIF, Score=827, Pubmed Id: 17632511, UMLKSK CUI: C0029454 Study reports mutations in the gene encoding RANKL (receptor activator of nuclear factor-KB ligand) in six individuals with autosomal recessive osteopetrosis whose bone biopsy specimens lacked osteoclasts
Human	MITF	4286	microphthalmia-associated transcription factor	GAD, Score=1000, Pubmed Id: 10385915, UMLKSK CUI: C0029454 Title:Microphthalmia-associated transcription factor (MITF) locus lacks linkage to human vitiligo or osteopetrosis: an evaluation.\|Association:Not Found\|Conclusion:Not Found
Human	LRP5	4041	low density lipoprotein receptor-related protein 5	OMIM, Score=790, UMLKSK CUI: C0029454 Allelic with osteoporosis-pseudoglioma syndrome ({259770}), van Buchem type 2 ({607636}), autosomal dominant osteosclerosis ({144750}), type I osteopetrosis ({607634}) OMIM, Score=790, UMLKSK CUI: C0029454 Allelic with type I osteopetrosis ({607634}), osteoporosis-pseudoglioma ({259770}), high bone mass ({601884}), autosomal dominant endosteal hyperostosis ({144750}) OMIM, Score=790, UMLKSK CUI: C0029454 Allelic with type I osteopetrosis ({607634}), osteoporosis-pseudoglioma ({259770}), type II van Buchem disease ({607636}), and high bone mass ({601884})
Human	CLCN7	1186	chloride channel, voltage-sensitive 7	GENERIF, Score=827, Pubmed Id: 17164308, UMLKSK CUI: C0029454 Autosomal dominant osteopetrosis caused by mutations in the CLCN7 gene is a frequently symptomatic disease manifested by a high rate of fracture, osteomyelitis, visual loss, and occasional bone marrow failure GENERIF, Score=827, Pubmed Id: 12929941, UMLKSK CUI: C0029454 mutations in the CICN7 gene are responsible for autosomal dominant osteopetrosis, type II, an uncommon sclerosing bone disorder OMIM, Score=1000, UMLKSK CUI: C0029454 Allelic with osteopetrosis ({259700}) GENERIF, Score=1000, Pubmed Id: 16368748, UMLKSK CUI: C0029454 Significant association of CLCN7 polymorphisms with the variance of bone density in postmenopausal women with osteopetrosis GENERIF, Score=861, Pubmed Id: 14584882, UMLKSK CUI: C0029454 ClCN7 mutations have roles in severe recessive, dominant, and intermediate osteopetrosis GENERIF, Score=812, Pubmed Id: 12522560, UMLKSK CUI: C0029454 clcn7 gene mutation is associated with intermediate autosomal recessive osteopetrosis
Human	CLCN1	1180	chloride channel, voltage-sensitive 1	GENERIF, Score=1000, Pubmed Id: 14564431, UMLKSK CUI: C0029454 Osteopetrosis, with unusual clinical manifestations, was caused by a mutation in CLCN
Human	ACP5	54	acid phosphatase 5, tartrate resistant	GENERIF, Score=694, Pubmed Id: 17997709, UMLKSK CUI: C0029454 heterozygous mutation (R714C) of the osteopetrosis gene, pleckstrin homolog domain containing family M (with run domain) member 1 (PLEKHM1), impairs vesicular acidification and increases TRACP secretion in osteoclasts

XRefs (1)

XRef Types:

cui : 1

ToppGene Datasets:

none : 1

ToppGene Datasets	XRef Type	XRef Id	XRef	Values	Source	Top % Rank
	CUI	C0029454	Osteopetrosis	0		self

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