Workshop demonstration
This page outlines a list of questions, relation between concept types and concepts with their sources.
Questions
(many of the questionsare taken from http://esw.w3.org/topic/HCLSIG/PharmaOntology/Roles)
Higher priority
Q34. Tell me everything we know about this target? [C1-17]
Q35.1 What types of cancer are most common in COPD patients?
Q35.2 Are these cancer types more prevalent in COPD patients than in the general population?
Q35.3 Which of these cancer types are related to smoking?
Q1. How is this therapy/compound different from existing therapies/compounds? [R4]
Q6. What subset of the population is most likely to have a success outcome from this medication based on gene expression and other molecular profiles? [R5], {R17], [R18], [R19]
Q9. What is the function of this target (gene/protein/phenotype)? [R8]
Q15. What targets are associated with this disease? [R7]
Q16. What experiments have been conducted on this target (gene/protein/phenotype)? [R14]
Q17. What active compounds or structures affect this target? [R7]
Q18. What subpopulation demographics are associated with this disease? (WP7b)
Q19. What are the current hot research topic areas for disease x? [R10[C10] + timelines]
Q20. What is the disease phenotype? [R10[C10]]
Q22. Who are the opinion leaders for a therapeutic area/drug/pathway based on literature and presentations? [R10[C16]]
Q25. Which animal species has the closest genome for the pathway/target of this disease? (to be considered)
Q30. What side effects are seen in therapies that affect this target? [R7], [R19]
Q33. What are the current hot research topic areas for disease x? [R10]- disease, [R10]- all other biological entities + timeline
Normal priority
Q7. What can we learn from previous targets/diseases? [R2, R4, R7]
Q10. What are the gene regulatory regions for this target? [R9]
Q11. What articles are available for this target? [R10]
Q12. Where is this gene expressed? [R11]
Q13. What is the gene expression in this tissue? [R13]
Q23. What are the related target and pathway for a specific disease [R16, R7, R2]
Q26. Find all the experiments that were done using my sample [R10]- cell lines/tissue/organ, [R10]- experiment/assay
Q28. What experiments have been conducted on this target (gene/protein/phenotype)? [R10]- gene/protein/phenotype, [R10]- experiment/assay
Q29. What experiments have altered the same pathway as this gene? [R10]- pathway, [R10]- experiment/assay
Lower priority
Q2. Provide a list of drugs approved by the FDA, EMEA and/or Japan for disease x. [R3]
Q3. Of drugs from either the same or different company for the same indication, are they approved in the same target region of interest – US or Global? [R1, R2, R3]
Q4. What is the delivery method and dosing of the drug? [R1]
Q5. What generic drugs exist for the same indication? [R2]
Q8. Tell me everything we know about a gene? [C1]
Q31. What are the alternative names for the disease/condition? [C10] disease ontology
Q32. What are the alternative names for the symptom? [C10] symptom ontology
Not yet prioritized for various reasons
Q14. Get all the interactions for X enzymes that are involved in Colon cancer. For all these genes, get the expression and aCGH values for all colon cancer samples [R2, R8, R13]
Q21. Do proteomic assays of tumor material and serum samples identify patterns reflecting outcomes? [R15]
Q24. How do the pathways, receptors and the drug response genes from the 5 different schizophrenia drugs compare? [R16, R7, R2]
Q27. Find all samples which are grade III colorectal cancer. For these sample, retrieve the expression, mutation and aCGH data [GEO]
Relations
R1. Company-Drug - FDA/WHO? - AZ
R2. Drug-(Disease/Indication) - ?DrugBank? - ONTO (IE)
R3. Regulator-Drug - ? - AZ
R4. Drug-MOA - ?DrugBank - OK
R5. Experiment(study) <> Disease -
R6. Drug-Compound type - ?DrugBank - OK
R7. Drug-target - ?DrugBank, KEGG? - Partial
R8. Target-(Gene-Protein-Phenotype; genomic info) - ?DrugBank - OK
R9. Gene regulation-Target [Transfac] - AZ
R10. Document-any other concept - ONTO (IE)
R11. Gene-Tissue (Uniprot?, Unigene) - AZ (high complexity)
R12. Gene-Gene [ortholog, homology] (Homologene, iProClass + many more) - ONTO (moderate complexity)
R13. (Sample/Tissue/Gene) - NCBI Geo - Evaluate (high complexity; AZ interaction)
R14. Experiment-Target (information extraction?) - WP7b/Sheffield to revise the requirements
R15. Protein-Population profile (NCBI Geo?, 2DPage) - Evaluate (high complexity; AZ interaction)
R16. Target-(gene/protein)-Interaction-Pathway - OK
R17. Disease <> Treatment (drug)
R18. Treatment(drug) <> Outcome
R19. Treatment(drug) <> Adverse effect
Concept
C1. Antibodies, immune response (low priority; is it possible to get a list of antibodies?)
C2. Exon (?GeneBank - analyze how to include huge structured data sources with no inference)
C3. SNP (HapMap/DBSNP - same as ?GeneBank)
C4. Gene
C5. Comapny (Dbpedia?)
C6. Treatment(Drug) (???)
C7. Regulator (WHO?)
C8. MOA (unstructured text/ChEBI/Chembase)
C9. Population profile (unstructured text/NCBI Geo?)
C10. Disease(Phenotype) (???)
C11. Compound (DrugBank/ChEBI/Chembase/CAS [not free])
C12. Target (?DrugBank)
C13. Document (pubmed, patentm ...)
C14. Patient data (not public)
C15. Experiment (MO, UMLS???)
C16. Pathway
C17. Outcome