Text file describing the protocol for the experiment, including the order of workflow execution.
Text file describing the background of the experiment, and the formulated hypothesis.
Excel file comparing the results from the workflows.
High-level overview of experiment and order of workflow execution.
set Match SNPs with concept profiles find
Science and technology/Natural science/Biology/Palaeontology
List concept sets Match SNPs with concept profiles Find supporting literature
rs174547 DKFZP434K028 -1 rs174547 DAGLA path:hsa04723 Retrograde endocannabinoid signaling - Homo sapiens (human) rs174547 C11orf9 -1 rs174547 C11orf10 -1 rs174547 FEN1 path:hsa03030 DNA replication - Homo sapiens (human) rs174547 FEN1 path:hsa03410 Base excision repair - Homo sapiens (human) rs174547 FEN1 path:hsa03450 Non-homologous end-joining - Homo sapiens (human) rs174547 FADS2 path:hsa00592 alpha-Linolenic acid metabolism - Homo sapiens (human) rs174547 FADS2 path:hsa01040 Biosynthesis of unsaturated fatty acids - Homo sapiens (human) rs174547 FADS2 path:hsa03320 PPAR signaling pathway - Homo sapiens (human) rs174547 MIR1908 -1 rs174547 FADS1 path:hsa01040 Biosynthesis of unsaturated fatty acids - Homo sapiens (human) rs174547 FADS3 -1 rs174547 RAB3IL1 -1 rs174547 MIR611 -1 rs2014355 CABP1 -1 rs2014355 MLEC -1 rs2014355 UNC119B -1 rs2014355 ACADS path:hsa00071 Fatty acid metabolism - Homo sapiens (human) rs2014355 ACADS path:hsa00280 Valine rs2014355 ACADS leucine and isoleucine degradation - Homo sapiens (human) rs2014355 ACADS path:hsa00650 Butanoate metabolism - Homo sapiens (human) rs2014355 ACADS path:hsa01100 Metabolic pathways - Homo sapiens (human) rs2014355 SPPL3 -1 rs2014355 MIR4700 -1 rs211718 SLC44A5 -1 rs211718 ACADM path:hsa00071 Fatty acid metabolism - Homo sapiens (human) rs211718 ACADM path:hsa00280 Valine rs211718 ACADM leucine and isoleucine degradation - Homo sapiens (human) rs211718 ACADM path:hsa00410 beta-Alanine metabolism - Homo sapiens (human) rs211718 ACADM path:hsa00640 Propanoate metabolism - Homo sapiens (human) rs211718 ACADM path:hsa01100 Metabolic pathways - Homo sapiens (human) rs211718 ACADM path:hsa03320 PPAR signaling pathway - Homo sapiens (human) rs2286963 KANSL1L -1 rs2286963 ACADL path:hsa00071 Fatty acid metabolism - Homo sapiens (human) rs2286963 ACADL path:hsa01100 Metabolic pathways - Homo sapiens (human) rs2286963 ACADL path:hsa03320 PPAR signaling pathway - Homo sapiens (human) rs2286963 MYL1 -1 rs9393903 uncharacterized LOC100506409 -1 rs9393903 SYCP2L -1 rs9393903 ELOVL2 path:hsa00062 Fatty acid elongation - Homo sapiens (human) rs9393903 ELOVL2 path:hsa01040 Biosynthesis of unsaturated fatty acids - Homo sapiens (human) rs9393903 C6orf228 -1 rs9393903 ERVFRD-1 -1 rs2216405 CPS1 path:hsa00250 Alanine rs2216405 CPS1 aspartate and glutamate metabolism - Homo sapiens (human) rs2216405 CPS1 path:hsa00330 Arginine and proline metabolism - Homo sapiens (human) rs2216405 CPS1 path:hsa01100 Metabolic pathways - Homo sapiens (human) rs7156144 TMEM229B -1 rs7156144 PLEKHH1 -1 rs7156144 PIGH path:hsa00563 Glycosylphosphatidylinositol(GPI)-anchor biosynthesis - Homo sapiens (human) rs7156144 PIGH path:hsa01100 Metabolic pathways - Homo sapiens (human) rs7156144 -1 rs11158519 SYNE2 -1 rs168622 uncharacterized LOC100505515 -1 rs168622 SPTLC3 path:hsa00600 Sphingolipid metabolism - Homo sapiens (human) rs168622 SPTLC3 path:hsa01100 Metabolic pathways - Homo sapiens (human) rs8396 RXFP1 path:hsa04080 Neuroactive ligand-receptor interaction - Homo sapiens (human) rs8396 C4orf46 -1 rs8396 ETFDH -1 rs8396 PPID -1 rs8396 FNIP2 -1 rs7094971 SLC16A9 -1 rs7094971 CCDC6 path:hsa05200 Pathways in cancer - Homo sapiens (human) rs7094971 CCDC6 path:hsa05216 Thyroid cancer - Homo sapiens (human) rs7094971 M1 -1 rs2046813 SLED1 -1 rs2046813 uncharacterized LOC100506229 -1 rs2046813 ACSL1 path:hsa00071 Fatty acid metabolism - Homo sapiens (human) rs2046813 ACSL1 path:hsa01100 Metabolic pathways - Homo sapiens (human) rs2046813 ACSL1 path:hsa03320 PPAR signaling pathway - Homo sapiens (human) rs2046813 ACSL1 path:hsa04146 Peroxisome - Homo sapiens (human) rs2046813 ACSL1 path:hsa04920 Adipocytokine signaling pathway - Homo sapiens (human) rs2046813 MIR3945 -1 rs2046813 MIR4455 -1 rs603424 uncharacterized LOC100653313 -1 rs603424 uncharacterized LOC100652751 -1 rs603424 CHUK path:hsa04010 MAPK signaling pathway - Homo sapiens (human) rs603424 CHUK path:hsa04062 Chemokine signaling pathway - Homo sapiens (human) rs603424 CHUK path:hsa04064 NF-kappa B signaling pathway - Homo sapiens (human) rs603424 CHUK path:hsa04210 Apoptosis - Homo sapiens (human) rs603424 CHUK path:hsa04380 Osteoclast differentiation - Homo sapiens (human) rs603424 CHUK path:hsa04620 Toll-like receptor signaling pathway - Homo sapiens (human) rs603424 CHUK path:hsa04621 NOD-like receptor signaling pathway - Homo sapiens (human) rs603424 CHUK path:hsa04622 RIG-I-like receptor signaling pathway - Homo sapiens (human) rs603424 CHUK path:hsa04623 Cytosolic DNA-sensing pathway - Homo sapiens (human) rs603424 CHUK path:hsa04660 T cell receptor signaling pathway - Homo sapiens (human) rs603424 CHUK path:hsa04662 B cell receptor signaling pathway - Homo sapiens (human) rs603424 CHUK path:hsa04920 Adipocytokine signaling pathway - Homo sapiens (human) rs603424 CHUK path:hsa05120 Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human) rs603424 CHUK path:hsa05131 Shigellosis - Homo sapiens (human) rs603424 CHUK path:hsa05142 Chagas disease (American trypanosomiasis) - Homo sapiens (human) rs603424 CHUK path:hsa05145 Toxoplasmosis - Homo sapiens (human) rs603424 CHUK path:hsa05160 Hepatitis C - Homo sapiens (human) rs603424 CHUK path:hsa05162 Measles - Homo sapiens (human) rs603424 CHUK path:hsa05166 HTLV-I infection - Homo sapiens (human) rs603424 CHUK path:hsa05168 Herpes simplex infection - Homo sapiens (human) rs603424 CHUK path:hsa05169 Epstein-Barr virus infection - Homo sapiens (human) rs603424 CHUK path:hsa05200 Pathways in cancer - Homo sapiens (human) rs603424 CHUK path:hsa05212 Pancreatic cancer - Homo sapiens (human) rs603424 CHUK path:hsa05215 Prostate cancer - Homo sapiens (human) rs603424 CHUK path:hsa05220 Chronic myeloid leukemia - Homo sapiens (human) rs603424 CHUK path:hsa05221 Acute myeloid leukemia - Homo sapiens (human) rs603424 CHUK path:hsa05222 Small cell lung cancer - Homo sapiens (human) rs603424 CWF19L1 -1 rs603424 BLOC1S2 -1 rs603424 PKD2L1 -1 rs603424 SCD path:hsa01040 Biosynthesis of unsaturated fatty acids - Homo sapiens (human) rs603424 SCD path:hsa03320 PPAR signaling pathway - Homo sapiens (human) rs603424 SNORA12 -1 rs272889 DKFZp779A135 -1 rs272889 P4HA2 path:hsa00330 Arginine and proline metabolism - Homo sapiens (human) rs272889 P4HA2 path:hsa01100 Metabolic pathways - Homo sapiens (human) rs272889 PDLIM4 -1 rs272889 SLC22A4 -1 rs272889 SLC22A5 -1 rs272889 MIR3936 -1 rs541503 HSD3BP4 -1 rs541503 FLJ41173 -1 rs541503 ZNF697 -1 rs541503 PHGDH path:hsa00260 Glycine rs541503 PHGDH serine and threonine metabolism - Homo sapiens (human) rs541503 PHGDH path:hsa01100 Metabolic pathways - Homo sapiens (human) rs541503 HMGCS2 path:hsa00072 Synthesis and degradation of ketone bodies - Homo sapiens (human) rs541503 HMGCS2 path:hsa00280 Valine rs541503 HMGCS2 leucine and isoleucine degradation - Homo sapiens (human) rs541503 HMGCS2 path:hsa00650 Butanoate metabolism - Homo sapiens (human) rs541503 HMGCS2 path:hsa00900 Terpenoid backbone biosynthesis - Homo sapiens (human) rs541503 HMGCS2 path:hsa01100 Metabolic pathways - Homo sapiens (human) rs541503 HMGCS2 path:hsa03320 PPAR signaling pathway - Homo sapiens (human)
FUNCTIONAL ANNOTATION OF SINGLE NUCLEOTIDE POLYMORHPISMS USING NEXT-GENERATION TEXT MINING AND CURATED METABOLIC PATHWAY DATABASES RESEARCH OBJECT
This research object implements the concept profile matching pipeline in the knowledge discovery tool Anni (http://biosemantics.org/anni), and adapts it to interpret the top SNPs from a GWAS. The underlying literature and concept profile databases are the same as the for the current version of Anni (2.1). The pack consists of three main workflows (http://www.myexperiment.org/workflows/2999, http://www.myexperiment.org/workflows/2973, http://www.myexperiment.org/workflows/2972). Workflow 2999 returns a list of available concept sets to match the SNPs against. As an example, the concept set GO biological processes is used. Workflow 2973 consist of nine nested workflows (eight different components in the pack, for which one is used twice within the main workflow for different purposes). It reuses the SNP to Entrez gene identifier part of this workflow: http://www.myexperiment.org/workflows/3124, here implemented as a separate workflow (http://www.myexperiment.org/workflows/2971). Workflow 2973 takes a SNP ID and a set of GO biological processes as input together with a set of parameter settings. The outputs give the following information: 1) information about the GO biological process with the highest matching score against the SNPs, 2) if there are any co-occurring documents supporting this finding, and 3) the concepts contributing most to the match (intermediate concepts). The output parameters can be saved in Taverna as an Excel sheet together with the input parameters for interpretation. Documents supporting the relation with the intermediate concepts contributing most to the match can be retrieved with workflow http://www.myexperiment.org/workflows/2972.
Functional annotation of SNPs using next-generation text mining
Described in myExperiment pack number 282
Kristina Hettne. "Functional annotation of SNPs using next-generation text mining." ROHub. Dec 14 ,2012. https://w3id.org/ro-id/1463b613-f7f7-4f25-b7ad-e2bfddacb732.
Science and technology/Technology and engineering/IT-computer sciences
The pack consists of three main workflows (http://www.myexperiment.org/workflows/2999, http://www.myexperiment.org/workflows/2973, http://www.myexperiment.org/workflows/2972). Workflow 2999 returns a list of available concept sets to match the SNPs against.
Functional annotation of single nucleotide polymorphisms (SNPs) using next-generation text mining and curated metabolic pathway databases.
Functional annotation of SNPs using next-generation text mining.
The EntrezGene id is used to query the Anni concept database to retrieve the internal concept id, which is used to retrieve the concept profile for the concept from the concept profile database.
This research object implements the concept profile matching pipeline in the knowledge discovery tool Anni (http://biosemantics.org/anni), and adapts it to interpret the top SNPs from a GWAS.
Science and technology/Social sciences/Philosophy
Arts, culture and entertainment/Arts and entertainment/Literature/Non-fiction
Science and technology/Social sciences/Anthropology
mathematical and computer sciences (general)
Economy, business and finance/Economic sector/Chemicals/Organic chemical
Science and technology/Natural science/Biology/Genetics