User:ProteinBoxBot/Phase 3

Overview

The goal of this phase of the ProteinBoxBot is to expand beyond the genes and proteins maintained in the Gene Wiki project to other biomedical concepts. Specifically, we are targeting human diseases and phenotypes, and drugs/compounds. Additional organization around SNPs and pathways are a possibility as well. Please add your ideas and suggestions below and/or contribute to the talk page!

Notes

• User:ProteinBoxBot currently runs every two days to maintain gene/protein infoboxes{{GNF Protein box}}, and a similar time scale should be possible on all templates/parameters mentioned below.
• All data in this Phase 3 proposal will likely go into Wikidata. Discussion of that effort can be found at d:WD:MBTF.

Disease

• Existing template: {{Infobox disease}}
• Prototype template: {{Infobox_disease/sandbox2}}
• Proposed fields to add/maintain:

Parameter	Description	In existing template	Reference	Source of mappings (counts)
Name	Disease name	yes	OMIM, Disease Ontology	(8699)
synonyms	Disease synonyms	no	OMIM, Disease Ontology	(17653)
Image	Relevant images	yes
OMIM	OMIM ID	yes	http://www.omim.org	(1749)
Disease Ontology	Disease Ontology link	no	http://disease-ontology.org/	(8699)
classification	Disease classification	no
Related genes	Relevant genes/proteins	no	Neurocarta, CTD, UniProt, OMIM, Orphanet, and/or GWAS Catalog
Compounds/drugs	Relevant drugs/compounds	no	Drugbank, PubChem, CTD
phenotypes	Relevant phenotypes	no	Human Phenotype Ontology
DiseasesDB	DiseasesDB ID	yes	http://www.diseasesdatabase.com/
ICD-10	ICD-10 ID	yes	http://apps.who.int/classifications/icd10/browse/2010/en
ICD-9	ICD-9 ID	yes	http://www.cdc.gov/nchs/icd/icd9.htm	(3335)
MedlinePlus	MedlinePlus ID	yes	http://www.nlm.nih.gov/medlineplus/
eMedicine	eMedicine ID	yes	http://emedicine.medscape.com/
MeSH	MeSH classification	yes	http://www.ncbi.nlm.nih.gov/mesh	(3221)
UMLS_CUI	UMLS CUI identifier	no	e.g., http://ncimeta.nci.nih.gov/ncimbrowser	(8390)
Orphanet	Orphanet ID	no	http://www.orpha.net
GeneReviews	Relevant GeneReviews	yes	http://www.ncbi.nlm.nih.gov/books/NBK1116/
MalaCards	Disease Name	no	http://www.malacards.org/

Examples

• Cystic fibrosis: single OMIM entry, no phenotypic series
• Sly syndrome: matches a single OMIM entry in a broader phenotypic series
• Sanfilippo syndrome: matches multiple OMIM entries, a subset of a phenotypic series
• Coenzyme Q10 deficiency: matches multiple OMIM entries comprising an entire phenotypic series
• Melanoma: complex disease with multiple OMIM matches?

{{Infobox medical condition/sandbox2 | Name = Cystic fibrosis | Image = ClubbingCF.JPG | Alt = | Caption = [[Nail clubbing|Clubbing]] in the fingers of a person with cystic fibrosis | DiseasesDB = 3347 | MalaCards = CYS001 | ICD10 = {{ICD10|E|84||e|70}} | ICD9 = {{ICD9|277.0}} | ICDO = | OMIM = 219700 | MedlinePlus = 000107 | eMedicineSubj = ped | eMedicineTopic = 535 | MeshID = D003550 | GeneReviewsID = | GeneReviewsName = }}

{{Infobox_disease/sandbox2 | Name = Sly syndrome | Image = | Caption = | DiseasesDB = 8389 | MalaCards = CYS001 | ICD10 = {{ICD10|E|76|2|e|70}} | ICD9 = {{ICD9|277.5}} | ICDO = | OMIM = 253220 | DO = 12803 | MedlinePlus = | eMedicineSubj = ped | eMedicineTopic = 858 | MeshID = D016538 | Synonyms = MUCOPOLYSACCHARIDOSIS TYPE VII | genes = [[GUSB]]<ref>{{cite journal|authors=Vervoort R; Islam MR; Sly WS; Zabot MT; Kleijer WJ; Chabas A; Fensom A; Young EP; Liebaers I; Lissens W|title=Molecular analysis of patients with beta-glucuronidase deficiency presenting as hydrops fetalis or as early mucopolysaccharidosis VII |journal=American journal of human genetics|date=March 1996 |volume=58|issue=3|pages=457-71|pmid=8644704}}</ref> | Orphanet = 584 | classification = [[lysosomal storage disease]] | phenotypes = *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0000007 Autosomal recessive inheritance] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0000023 Inguinal hernia] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0000238 Hydrocephalus] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0000256 Macrocephaly] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0000272 Malar flattening] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0000280 Coarse facial features] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0000365 Hearing impairment] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0000470 Short neck] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0000768 Pectus carinatum] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0000926 Platyspondyly] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0000943 Dysostosis multiplex] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001004 Lymphedema] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001007 Hirsutism] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001249 Intellectual disability] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001252 Muscular hypotonia] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001371 Flexion contracture] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001376 Limitation of joint mobility] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001392 Abnormality of the liver] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001537 Umbilical hernia] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001541 Ascites] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001654 Abnormality of the heart valves] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001744 Splenomegaly] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001789 Hydrops fetalis] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001840 Metatarsus adductus] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0001883 Talipes] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0002103 Abnormality of the pleura] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0002180 Neurodegeneration] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0002205 Recurrent respiratory infections] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0002240 Hepatomegaly] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0002650 Scoliosis] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0002680 J-shaped sella turcica] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0003272 Abnormality of the hip bone] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0003311 Hypoplasia of the odontoid process] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0003375 Narrow greater sacrosciatic notches] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0003541 Urinary glycosaminoglycan excretion] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0004322 Short stature] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0004607 Anterior beaking of lower thoracic vertebrae] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0005619 Thoracolumbar kyphosis] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0006119 Proximal tapering of metacarpals] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0007759 Opacification of the corneal stroma] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0007957 Reduction of corneal clarity] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0008301 Dermatan sulfate excretion in urine] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0008430 Anterior beaking of lumbar vertebrae] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0008807 Acetabular dysplasia] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0008897 Postnatal growth retardation] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0010655 Epiphyseal stippling] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0100026 Arteriovenous malformation] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0100543 Cognitive impairment] *[http://bioportal.bioontology.org/ontologies/50173/?p=terms&conceptid=HP:0100625 Enlarged thorax] }}

{{Infobox medical condition/sandbox2 |Name = Sanfilippo Syndrome |Image = |Caption = |DiseasesDB = 29177 |ICD10 = {{ICD10|E|76|2|e|70}} |ICD9 = {{ICD9|277.5}} |ICDO = |MedlinePlus = 001210 |eMedicineSubj = ped |eMedicineTopic = 2040 |MeshID = D009084 |OMIM_table = {{infobox3cols | above = OMIM Phenotypic Series [http://omim.org/phenotypicSeries/607014] | label1 = MUCOPOLYSACCHARIDOSIS TYPE IIIA | data1a = {{OMIM2|252900}} | data1b = [[SGSH]] | label2 = MUCOPOLYSACCHARIDOSIS TYPE IIIB | data2a = {{OMIM2|252920}} | data2b = [[NAGLU]] | label3 = MUCOPOLYSACCHARIDOSIS TYPE IIIC | data3a = {{OMIM2|252930}} | data3b = [[HGSNAT]] | label4 = MUCOPOLYSACCHARIDOSIS TYPE IIID | data4a = {{OMIM2|252940}} | data4b = [[N-acetylglucosamine-6-sulfatase|GNS]] }} }}

{{Infobox medical condition/sandbox3 | Name = Coenzyme Q10 deficiency | Image = Ubiquinone.png | Alt = | Caption = Ubiquinone | DiseasesDB = 32701 | ICD10 = | ICD9 = | ICDO = | DO = 0050730 | OMIM = | OMIM_mult = | MedlinePlus = | eMedicineSubj = | eMedicineTopic = | MeshID = C564403 | genes = [[COQ2]]<ref>{{OMIM|607426}}</ref>, [[COQ6]]<ref>{{OMIM|614650}}</ref>, [[PDSS2]]<ref>{{OMIM|614652}}</ref>, [[PDSS1]]<ref>{{OMIM|614651}}</ref>, [[ADCK3]]<ref>{{cite journal|authors=Mollet J; Delahodde A; Serre V; Chretien D; Schlemmer D; Lombes A; Boddaert N; Desguerre I; de Lonlay P; de Baulny HO; Munnich A; Rötig A |title=CABC1 gene mutations cause ubiquinone deficiency with cerebellar ataxia and seizures |journal=American journal of human genetics|date=March 2008 |volume=82|issue=3|pages=623-30|pmid=18319072}}</ref><ref>{{OMIM|606980}}</ref>, [[COQ9]]<ref>{{OMIM|614654}}</ref> | drugs = [[Ubidecarenone]] | classification = inherited metabolic disorder | Orphanet = 35656 | OMIM_table = {{infobox3cols | above = OMIM Phenotypic Series [http://omim.org/phenotypicSeries/607426] | label18 = Coenzyme Q10 deficiency, primary, 1 | data18a = {{OMIM2|607426}} | data18b = [[COQ2]] | label19 = Coenzyme Q10 deficiency, primary, 2 | data19a = {{OMIM2|614651}} | data19b = [[PDSS1]] | label20 = Coenzyme Q10 deficiency, primary, 3 | data20a = {{OMIM2|614652}} | data20b = [[PDSS2]] | label21 = Coenzyme Q10 deficiency, primary, 4 | data21a = {{OMIM2|612016}} | data21b = [[CABC1]] | label22 = Coenzyme Q10 deficiency, primary, 5 | data22a = {{OMIM2|614654}} | data22b = [[COQ9]] | label23 = Coenzyme Q10 deficiency, primary, 6 | data23a = {{OMIM2|614650}} | data23b = [[COQ6]] }} }}

{{Infobox medical condition/sandbox2 |Name = Melanoma |Image = Melanoma.jpg |Caption = a melanoma |Width = 250 |DiseasesDB = 7947 |ICD10 = {{ICD10|C|43||c|43}} |ICD9 = {{ICD9|172.9}} |ICDO = {{ICDO|8720|3}} |OMIM = 155600 |MedlinePlus = 000850 |eMedicineSubj = derm |eMedicineTopic = 257 |eMedicine_mult = {{eMedicine2|med|1386}} {{eMedicine2|ent|27}} {{eMedicine2|plastic|456}} |MeshID = D008545 |BioVex |drugs = [[vemurafenib]], [[dacarbazine]], [[ipilimumab]], [[vemurafenib]], [[temozolomide]], [[proleukin]] |classification = [[cancer]] |DO = 1909 |subtypes = * [[amelanotic melanoma]] * [[epithelioid cell melanoma]] * [[familial melanoma]] * [[malignant spindle cell melanoma]] * [[melanomatosis]] }}

Drug/Compound

• Existing template: {{Drugbox}}
• Prototype template: {{Drugbox/sandbox2}}
• Proposed fields to add/maintain:

Parameter	Description	In existing template	Source
Trade name(s)	Brand/trade names	yes	DrugBank, PubChem
image	Chemical structure	yes	ChemSpider, ChEMBL
Mechanism	Mechanism of action	no
Biological_target	Links to relevant protein targets	no	Drugbank, PubChem, CTD, http://stitch.embl.de, http://sideeffects.embl.de/
Therapeutic_use	Links to relevant diseases	no	Drugbank, PubChem, CTD
Side effects	Side effects/ known drug interactions	no	http://sideeffects.embl.de/
AHFS/Drugs.com	FDA Professional Drug Information	yes	www.drugs.com
Legal status	Regulation of therapeutic goods	yes	http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.Search_Drug_Name
Pregnancy category	Relevant pregnancy category	yes	www.drugs.com
Routes	Route(s) of administration	yes	DrugBank, drugs.com
CAS number	CAS identifier	yes	https://www.cas.org/
ATC_prefix	ATC code	yes	http://www.whocc.no/atc_ddd_index/
ATC_suffix	ATC code	yes	http://www.whocc.no/atc_ddd_index/
PubChem	PubChem ID	yes	http://pubchem.ncbi.nlm.nih.gov/
ChemSpider	ChemSpider ID	yes	http://www.chemspider.com/
UNII	UNII ID	yes	http://fdasis.nlm.nih.gov/
DrugBank	DrugBank ID	yes	http://www.drugbank.ca/
ChEMBL	ChEMBL ID	yes	https://www.ebi.ac.uk/chembl/
ChEBI	ChEBI ID	yes	https://www.ebi.ac.uk/chebi
PDB ligand ID	PDB ID of related ligand	yes	http://ligand-expo.rcsb.org/
KEGG	Related KEGG pathway	yes	http://www.genome.jp/kegg/
Formula	Chemical formula	yes	PubChem, ChemSpider, ChEMBL, DrugBank
Mol. mass	Molecular mass	yes	PubChem, ChemSpider, ChEMBL, DrugBank
InChI	International Chemical Identifier	yes	PubChem, ChemSpider, ChEMBL, DrugBank

Data sources

• Drugbank (though note possible data quality issues with brand/trade names [1])
• PubChem (though note errors in how polymers are handled [2])
• Freebase (e.g., https://www.freebase.com/m/0hqvq1s), though ideally we work back to freebase's sources
• NDF-RT (Description FTP)

Examples

{{Drugbox/sandbox2 | drug_name = vemurafenib | verifiedrevid = 432742697 | image = PLX4032_BRAF_inhibitor.png <!--Clinical data--> | tradename = Zelboraf | licence_US = Vemurafenib | pregnancy_US = D | legal_US = Rx-only | routes_of_administration = Oral | Drugs.com = {{Drugs.com|pro|zelboraf}} | MedlinePlus = <!--Pharmacodynamic data--> | Therapeutic_use = [[Melanoma]] | Biological_target = [[BRAF (gene)|BRAF]] | MOA_text = [[Protein kinase inhibitor]] | PDB_ligand = 032 | PDB_complex = 3og7 <!--Identifiers--> | CAS_number = 1029872-54-5 | ATC_prefix = L01 | ATC_suffix = XE15 | PubChem = 42611257 | ChemSpiderID_Ref = {{chemspidercite|correct|chemspider}} | ChemSpiderID = 24747352 | ChEMBL = 1229517 | UNII = 207SMY3FQT <!--Chemical data--> | C=23 | H=18 | Cl=1 | F=2 | N=3 | O=3 | S=1 | molecular_weight = 489.92 g/mol | StdInChI_Ref = {{stdinchicite|correct|chemspider}} | StdInChI = 1S/C23H18ClF2N3O3S/c1-2-9-33(31,32)29-19-8-7-18(25)20(21(19)26)22(30)17-12-28-23-16(17)10-14(11-27-23)13-3-5-15(24)6-4-13/h3-8,10-12,29H,2,9H2,1H3,(H,27,28) | StdInChIKey_Ref = {{stdinchicite|correct|chemspider}} | StdInChIKey = GPXBXXGIAQBQNI-UHFFFAOYSA-N }} |} Genes/Proteins Existing template: {{GNF Protein box}} Prototype template: {{GNF Protein box/sandbox2}} Proposed fields to add: Links to relevant disease (with evidence and/or effect sizes) Links to relevant drugs/compounds Examples {{GNF_Protein_box/sandbox2 | Name = Glucuronidase, beta | image = Protein_GUSB_PDB_1bhg.png | image_source = [[Protein_Data_Bank|PDB]] rendering based on 1bhg. | PDB = {{PDB2|1BHG}}, {{PDB2|3HN3}} | HGNCid = 4696 | MGIid = 95872 | Symbol = GUSB | AltSymbols =; BG; MPS7 | IUPHAR = | ChEMBL = 2728 | OMIM = 611499 | ECnumber = 3.2.1.31 | Homologene = 37271 | GeneAtlas_image1 = PBB_GE_GUSB_202605_at_tn.png | GeneAtlas_image2 = | GeneAtlas_image3 = | Protein_domain_image = | Function = {{GNF_GO|id=GO:0004566 |text = beta-glucuronidase activity}} | Component = {{GNF_GO|id=GO:0043202 |text = lysosomal lumen}} {{GNF_GO|id=GO:0043231 |text = intracellular membrane-bounded organelle}} | Process = {{GNF_GO|id=GO:0005975 |text = carbohydrate metabolic process}} {{GNF_GO|id=GO:0006027 |text = glycosaminoglycan catabolic process}} {{GNF_GO|id=GO:0030203 |text = glycosaminoglycan metabolic process}} {{GNF_GO|id=GO:0030212 |text = hyaluronan metabolic process}} {{GNF_GO|id=GO:0030214 |text = hyaluronan catabolic process}} {{GNF_GO|id=GO:0044281 |text = small molecule metabolic process}} | Hs_EntrezGene = 2990 | Hs_Ensembl = ENSG00000169919 | Hs_RefseqmRNA = NM_000181 | Hs_RefseqProtein = NP_000172 | Hs_GenLoc_db = hg19 | Hs_GenLoc_chr = 7 | Hs_GenLoc_start = 65425671 | Hs_GenLoc_end = 65447301 | Hs_Uniprot = P08236 | Mm_EntrezGene = 110006 | Mm_Ensembl = ENSMUSG00000025534 | Mm_RefseqmRNA = NM_010368 | Mm_RefseqProtein = NP_034498 | Mm_GenLoc_db = mm9 | Mm_GenLoc_chr = 5 | Mm_GenLoc_start = 129989011 | Mm_GenLoc_end = 130003049 | Mm_Uniprot = P12265 | path = PBB/2990 | Diseases = [[Mucopolysaccharidosis_Type_VII]]<ref>{{cite journal|authors=Vervoort R; Islam MR; Sly WS; Zabot MT; Kleijer WJ; Chabas A; Fensom A; Young EP; Liebaers I; Lissens W |title=Molecular analysis of patients with beta-glucuronidase deficiency presenting as hydrops fetalis or as early mucopolysaccharidosis VII|journal=American journal of human genetics|date=March 1996 |volume=58|issue=3|pages=457-71|pmid=8644704}}</ref> }} References