Difference between revisions of "Johnllopez Week 14"
From LMU BioDB 2017
(Added table for what information needs to be pulled from where) |
(→Pulling Data: Added how to get the data) |
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'''NCBI''' | '''NCBI''' | ||
| − | *Locus tag | + | *Locus tag < Parse from page https://www.ncbi.nlm.nih.gov/gene/854068 |
| − | *Gene ID | + | *Gene ID < Parse from conversion algorithm |
'''UniProt''' | '''UniProt''' | ||
| − | *Protein type/name | + | *Protein type/name <Parse XML? |
| − | *Protein sequence | + | *Protein sequence <Parse XML |
| − | *Gene ID | + | *Gene ID <Parse XML |
| − | *Similar proteins | + | *Similar proteins <Could not find on XML, found on Page |
'''Ensembl''' | '''Ensembl''' | ||
| − | *DNA sequence | + | *DNA sequence < Pull from http://www.ensembl.org/Saccharomyces_cerevisiae/Transcript/Sequence_cDNA?db=core;g=YJL128C;r=X:178097-180103;t=YJL128C |
| − | *Gene description | + | *Gene description < Pulled from JSON |
| − | *Gene ID | + | *Gene ID < Pulled from JSON / Conversion Necessary |
'''SGD''' | '''SGD''' | ||
| − | *Gene ID | + | *Gene ID < Pulled from JSON/ Possible conversion necessary |
| − | *Gene expression | + | *Gene expression < NO IDEA HOW WE CAN PULL THIS |
| − | *Gene regulation | + | *Gene regulation <Pull from page https://www.yeastgenome.org/locus/S000005446 |
| − | *Gene ontology | + | *Gene ontology <SUummary in JSON |
'''JASPAR''' | '''JASPAR''' | ||
*Sequence logo | *Sequence logo | ||
*Frequency matrixon her | *Frequency matrixon her | ||
Revision as of 08:50, 30 November 2017
Pulling Data
Thanks to Corrine Wong, I was able to use the following table to figure out what processes had to be made in order to pull certain data from the functions:
NCBI
- Locus tag < Parse from page https://www.ncbi.nlm.nih.gov/gene/854068
- Gene ID < Parse from conversion algorithm
UniProt
- Protein type/name <Parse XML?
- Protein sequence <Parse XML
- Gene ID <Parse XML
- Similar proteins <Could not find on XML, found on Page
Ensembl
- DNA sequence < Pull from http://www.ensembl.org/Saccharomyces_cerevisiae/Transcript/Sequence_cDNA?db=core;g=YJL128C;r=X:178097-180103;t=YJL128C
- Gene description < Pulled from JSON
- Gene ID < Pulled from JSON / Conversion Necessary
SGD
- Gene ID < Pulled from JSON/ Possible conversion necessary
- Gene expression < NO IDEA HOW WE CAN PULL THIS
- Gene regulation <Pull from page https://www.yeastgenome.org/locus/S000005446
- Gene ontology <SUummary in JSON
JASPAR
- Sequence logo
- Frequency matrixon her
