User: mk

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mk150
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Posts by mk

<prev • 39 results • page 1 of 4 • next >
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Comment: C: what is the uniprot RDF entity for "uniprot accession"?
... thanks for the thorough answer ...
written 3 days ago by mk150
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what is the uniprot RDF entity for "uniprot accession"?
... All proteins on UniProt have a unique accession number. Ex "O15169" is the accession for human Axin 1. Other RDF stores referring to proteins on UniProt use this accession (eg [Pathway Commons reference][2]) [This document][1] describes the RDF schema for UniProt. Where is the UniProt accession ...
rdf uniprot written 4 days ago by mk150 • updated 3 days ago by me720
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error when trying to perform a federated query in Pathway Commons SPARQL endpoint
... The following query works at [Pathway Commons SPARQL endpoint][1] and returns all proteins that form complexes controlling Wnt signaling pathways: PREFIX rdf: PREFIX owl: PREFIX rdfs: PREFIX xsd: PREFIX bp: PREFIX up: SELECT ?pathway ?protein ?eref WHERE { ...
rdf biopax pathway commons sparql uniprot written 4 days ago by mk150 • updated 1 day ago by me720
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Answer: A: Are federated SPARQL queries pointless with the Pathway Commons BioPAX represent
... The answer to (2) is apparently "yes": ["Pathway Commons integrates a number of pathway and molecular interaction databases supporting BioPAX and PSI-MI formats into one large BioPAX model"][1] [1]: https://www.pathwaycommons.org/pc2/ ...
written 7 days ago by mk150
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Are federated SPARQL queries pointless with the Pathway Commons BioPAX representation?
... Wikipathways, [Reactome][1], and [Pathway Commons][2] all contain pathway information which is supported in BioPAX 3.0. All three publish BioPAX representations of their data. [Wikipathways][3] and [Pathway Commons][4] allow access to a 'release' of their respective representations via HTTP server ...
wikipathways reactome biopax sparql ontology written 7 days ago by mk150
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database of ligand->receptor->TF(or transcriptional target)
... Is there an online database or package-based tool to find interactions where each record has at least: 1. ligand gene 2. receptor gene 3. transcriptional target 4. direction of regulation [is (4) up or down in response to (1,2)]\* \* (4) can just be omitted if (3) is always up in a certain dat ...
database signaling written 11 days ago by mk150
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Comment: C: censoring time for ICGC records with no followup or date of death?
... Indeed, I will update once I receive a response from their support team. ...
written 12 weeks ago by mk150
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Comment: C: ICGC mRNA sequencing data: where is the documentation on analysis_id?
... Thanks, Kevin I have emailed support. They are swamped due to lock down. Agree regarding the abbreviation, that's how I am proceeding in the mean time. ...
written 12 weeks ago by mk150
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censoring time for ICGC records with no followup or date of death?
... Looking at the ICGC release of PACA-CA (various stages of pancreatic carcinoma, Canada) there are numerous censored records (no death date) without a followup time. Is there a default censoring time for ICGC studies? Here are some examples ([PACA-CA][1]): patient ID | followup | death time ...
icgc survival cancer written 3 months ago by mk150
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Comment: C: Entrez e-utils reference for ensembl ids
... awesome, didn't know that ENSG ids were accepted ...
written 3 months ago by mk150

Latest awards to mk

Good Question 6 days ago, asked a question that was upvoted at least 5 times. For Mapping Ensembl Gene IDs with dot suffix
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Linking patient survival to gene-set analysis
Appreciated 15 months ago, created a post with more than 5 votes. For Mapping Ensembl Gene IDs with dot suffix
Popular Question 15 months ago, created a question with more than 1,000 views. For Linking patient survival to gene-set analysis
Popular Question 20 months ago, created a question with more than 1,000 views. For GDC API query to map HT-seq FPKM UUID to a Case UUID
Popular Question 21 months ago, created a question with more than 1,000 views. For GDC API query to map HT-seq FPKM UUID to a Case UUID
Popular Question 22 months ago, created a question with more than 1,000 views. For GDC API query to map HT-seq FPKM UUID to a Case UUID
Student 22 months ago, asked a question with at least 3 up-votes. For Mapping Ensembl Gene IDs with dot suffix
Scholar 2.7 years ago, created an answer that has been accepted. For A: Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assa

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