User:ProteinBoxBot/Phase 3

From Wikipedia, the free encyclopedia
Jump to: navigation, search

Overview[edit]

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[edit]

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[edit]

Examples[edit]

  • 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 = *{{HPO|HP:0000007|Autosomal recessive inheritance}} *{{HPO|HP:0000023|Inguinal hernia}} *{{HPO|HP:0000238|Hydrocephalus}} *{{HPO|HP:0000256|Macrocephaly}} *{{HPO|HP:0000272|Malar flattening}} *{{HPO|HP:0000280|Coarse facial features}} *{{HPO|HP:0000365|Hearing impairment}} *{{HPO|HP:0000470|Short neck}} *{{HPO|HP:0000768|Pectus carinatum}} *{{HPO|HP:0000926|Platyspondyly}} *{{HPO|HP:0000943|Dysostosis multiplex}} *{{HPO|HP:0001004|Lymphedema}} *{{HPO|HP:0001007|Hirsutism}} *{{HPO|HP:0001249|Intellectual disability}} *{{HPO|HP:0001252|Muscular hypotonia}} *{{HPO|HP:0001371|Flexion contracture}} *{{HPO|HP:0001376|Limitation of joint mobility}} *{{HPO|HP:0001392|Abnormality of the liver}} *{{HPO|HP:0001537|Umbilical hernia}} *{{HPO|HP:0001541|Ascites}} *{{HPO|HP:0001654|Abnormality of the heart valves}} *{{HPO|HP:0001744|Splenomegaly}} *{{HPO|HP:0001789|Hydrops fetalis}} *{{HPO|HP:0001840|Metatarsus adductus}} *{{HPO|HP:0001883|Talipes}} *{{HPO|HP:0002103|Abnormality of the pleura}} *{{HPO|HP:0002180|Neurodegeneration}} *{{HPO|HP:0002205|Recurrent respiratory infections}} *{{HPO|HP:0002240|Hepatomegaly}} *{{HPO|HP:0002650|Scoliosis}} *{{HPO|HP:0002680|J-shaped sella turcica}} *{{HPO|HP:0003272|Abnormality of the hip bone}} *{{HPO|HP:0003311|Hypoplasia of the odontoid process}} *{{HPO|HP:0003375|Narrow greater sacrosciatic notches}} *{{HPO|HP:0003541|Urinary glycosaminoglycan excretion}} *{{HPO|HP:0004322|Short stature}} *{{HPO|HP:0004607|Anterior beaking of lower thoracic vertebrae}} *{{HPO|HP:0005619|Thoracolumbar kyphosis}} *{{HPO|HP:0006119|Proximal tapering of metacarpals}} *{{HPO|HP:0007759|Opacification of the corneal stroma}} *{{HPO|HP:0007957|Reduction of corneal clarity}} *{{HPO|HP:0008301|Dermatan sulfate excretion in urine}} *{{HPO|HP:0008430|Anterior beaking of lumbar vertebrae}} *{{HPO|HP:0008807|Acetabular dysplasia}} *{{HPO|HP:0008897|Postnatal growth retardation}} *{{HPO|HP:0010655|Epiphyseal stippling}} *{{HPO|HP:0100026|Arteriovenous malformation}} *{{HPO|HP:0100543|Cognitive impairment}} *{{HPO|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[edit]

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[edit]

Examples[edit]

{{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[edit]

  • 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[edit]

{{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[edit]