Midterm Project

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Midterm Project
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Database Schema

• GeneIDTable
• Information about gene and corresponding
  protein
• gene_id, gene_name, gene_seq, protein_id,
  protein_name, protein_seq, gene_type
• gene_id primary key (type varchar(255))
• gene_type type varchar(255)
• All other entries are of type longtext

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Database Schema

• GeneFuncTable
• Information about gene functions
• gene_id, gene_fun, comment
• gene_id foreign key
• All entries are of type longtext

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Database Schema

• ProteinFuncTable
• Information about protein functions
• protein_id, protein_fun, comment
• All entries are of type longtext

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Database Schema

• PathwayFuncTable
• Information about pathway functions
• pathway_id, pathway_name, pathway_fun,
  pathway_loc, comment
• All entries are of type longtext

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Database Schema

• PathwayTable
• Information about gene pathway association
• gene_id, pathway_id
• gene_id type varchar(255)
• pathway_id type longtext

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Database Schema

• BiologicalProcessTable
• Gene Ontology related table
• Information about biological processes of a
  particular gene
• gene_id, GO_num, biological_process
• gene_id foreign key (type varchar(255))
• All other entries are of type longtext

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Database Schema

• CellularComponentTable
• Gene Ontology related table
• Information about cellular component
• gene_id, GO_num, cellular_component
• gene_id foreign key (type varchar(255))
• All other entries are of type longtext

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Database Schema

• MolecularFunctionTable
• Gene Ontology related table
• Information about molecular functions
• gene_id, GO_num, molecular_function
• gene_id foreign key (type varchar(255))
• All entries are of type longtext

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Steps to Follow Step 1

• Get the RefSeq Accession Number of your species
  from the NCBI Genome database
• e.g. NC_000913 for Escherichia Coli K12

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Steps to Follow Step 2

• Downloading files needed using the NCBI ftp site
  (ftp//ftp.ncbi.nlm.nih.gov)
• genomes/Bacteria/species name/RefSeq .gbk
  (main information for genes and proteins and GO
  functions)
• e.g. genomes/Bacteria/Escherichia_coli_k12/NC_0009
  13.gbk
• genomes/Bacteria/species name/RefSeq .ffn
  (gene sequence)
• e.g. genomes/Bacteria/Escherichia_coli_k12/NC_0009
  13.ffn

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Steps to Follow Step 3

• Go to KEGG selected organisms (http//www.genome.j
  p/kegg/catalog/org_list.html)
• Find your species and click the second column of
  the species (e.g. eco for E Coli)
• Go to pathway maps to get pathway information
  to put into the PathwayFunc table

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Steps to Follow Step 4

• Use eutils function of NCBI Entrez to get the
  file that contains gene pathway association
  (http//eutils.ncbi.nlm.nih.gov/entrez/eutils/)
• Use esearch to search your species in the gene
  database http//eutils.ncbi.nlm.nih.gov/entrez/eut
  ils/esearch.fcgi?dbdatabasetermqueryusehistory
  y
• Use efetch to fetch the result file
• http//eutils.ncbi.nlm.nih.gov/entrez/eutils/efetc
  h.fcgi?dbdatabaseWebEnvWebEnvStringquery_keyk
  ey

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Steps to Follow Step 5

• Edit .gbk file to remove the beginning and the
  end part
• Parse the .gbk and the .ffn file to fill all the
  tables except the PathwayFunc table and Pathway
  table
• Link to the sample parser file
• Parse.java

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Steps to Follow Step 6

• Parse the eutils resulting file to get the gene
  pathway association
• Link to the sample parsePath file
• ParsePath.java

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Database Name Format

• Example species Escherichia Coli K12
• Species name Escherichia_Coli_K12
• Database name escherichia_coli_k12

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Sample Output File

• outputFile.txt (output file after parsing .gbk
  and .ffn files)
• outputPath.txt (output file after parsing gene
  pathway association file)
• PathwayFunc.txt (output file after analyzing KEGG
  pathways)

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To Find the Number of Genes

• Search your species in NCBI gene database
• e.g. Escherichia Coli K12 orgn
• Check the number of genes in your result with
  this number

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• Submit your project (the 3 output files, the
  parsers if any changes) to
• vgummulu_at_cise.ufl.edu
• Any questions
• yizhang_at_cise.ufl.edu
• anupamd_at_ufl.edu