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	^[1] (8699)
`synonyms`	Disease synonyms	no	OMIM, Disease Ontology	^[1] (17653)
`Image`	Relevant images	yes
`OMIM`	OMIM ID	yes	http://www.omim.org	^[1] (1749)
`Disease Ontology`	Disease Ontology link	no	http://disease-ontology.org/	^[1] (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	^[1] (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	^[1] (3221)
`UMLS_CUI`	UMLS CUI identifier	no	e.g., http://ncimeta.nci.nih.gov/ncimbrowser	^[1] (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/

References

1 2 3 4 5 6 7 http://purl.obolibrary.org/obo/doid.obo

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 )
PubChem (though note errors in how polymers are handled )
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  | tradename = Zelboraf | licence_US = Vemurafenib | pregnancy_US = D | legal_US = Rx-only | routes_of_administration = Oral | Drugs.com = {{Drugs.com|pro|zelboraf}} | MedlinePlus =  | Therapeutic_use = [[Melanoma]] | Biological_target = [[BRAF (gene)|BRAF]] | MOA_text = [[Protein kinase inhibitor]] | PDB_ligand = 032 | PDB_complex = 3og7  | CAS_number = 1029872-54-5 | ATC_prefix = L01 | ATC_suffix = XE15 | PubChem = 42611257 | ChemSpiderID_Ref = {{chemspidercite|correct|chemspider}} | ChemSpiderID = 24747352 | ChEMBL = 1229517 | UNII = 207SMY3FQT  | 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

[doid.obo-1] 1 2 3 4 5 6 7 http://purl.obolibrary.org/obo/doid.obo

[1]