wiki:GritsTutorial_UpdateNamespaces

Updating Namespace Files

For updating the namespace files, one can run the main classes in the project NamespaceDataGeneration. This project has two folders rawFiles and processedFile. The rawFiles contains all the files that are directly downloaded from the internet and are available after unzipping them or copying them in text files. For each of the files there is a separate class with main method that can be run to obtain the processed file. The individual classes can be found in this package of the project. The processed files are stored inside the processedFile folder. One can copy these folders and put it directly in the namespace folder of the Sample project. To update all of them together one can run the NamespaceGenerator.java class inside this package which can generate all the processed files.

Here are the details for obtaining raw files for the respective classes of various namespaces that process them.

Cell Type

class : ExtractCellType.java
link : http://www.ontobee.org/browser/index.php?o=CL

File to be downloaded shown below with a red arrow




rawFileName : "cl.owl"

Compound

class : ExtractCompoundNames.java
link : ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/
zipped file : CID-Synonym-filtered.gz
rawFileName : "CID-Synonym-filtered" (After extracting from the zipped file "CID-Synonym-filtered.gz")

Disease

class : ExtractDiseaseType.java
link : http://www.ontobee.org/browser/index.php?o=DOID
rawFileName : "doid.owl"

Gene

class : ExtractGeneNames.java link : ftp://ftp.ncbi.nih.gov/gene/DATA/
zipped file : gene_info.gz
rawFileName : "gene_info" (After extracting from the zipped file "gene_info.gz")

Tissue

class : ExtractTissue.java
link : http://www.ontobee.org/browser/index.php?o=UBERON
rawFileName : "ext.owl"

Cell Line

class : ParseParentCellLineNamespace.java
link : http://grants.nih.gov/stem_cells/registry/current.htm
rawFileName : "parentCellLine.txt" (After pasting the html content in an empty textFile)

Species

class : ParseSpeciesNames.java
link : ftp://ftp.ncbi.nih.gov/pub/taxonomy
zipped file : taxdmp.zip
rawFileName : "names.dmp" (One of the file inside the zipped file "taxdmp.zip")

Anatomy

class : ExtractMeshTreeNames.java
link : ftp://nlmpubs.nlm.nih.gov/online/mesh/.asciimesh/d2015.bin
rawFileName : d2015.bin

downloaded through : https://www.nlm.nih.gov/cgi/request.meshdata
File to be downloaded from the link shown below with a red arrow




Last modified 6 years ago Last modified on 09/23/2015 10:20:07 PM

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