Functions for Fetching 'GeOMe-db' Data

The Genomic Observatory Metadatabase (GeOMe Database) is an open access repository for geographic and ecological metadata associated with sequenced samples. This package is used to retrieve GeOMe data for analysis. See < http://www.geome-db.org> for more information regarding GeOMe.


A set of R scripts for accessing and working with geome-db FIMS data from R

Installation

To get the current released version from CRAN :

install.packages("geomedb")

To get the current development version from github:

install.packages("devtools")
library(devtools)
install_github("biocodellc/fimsR-access")
library(geomedb)

Examples

To get a list of projects in the database:

project <- listProjects()

To get a list of expeditions for a project:

expeditions <- listExpeditions(1)

To get a list of entities available to query in geome:

entities <- listEntities()

To get a list of entities available to query for a specific project:

entities <- listEntities(1)

The query function will execute a query against the GeOMe database. The results are returned as a data.frame The most basic query will return all the samples in the database:

df <- queryMetadata('Sample')

The following query will return all samples for the expeditions "acaach_CyB_JD" and "acajap_CyB_JD"

df <- queryMetadata('Sample', projects=list(1), expeditions=list("acaach_CyB_JD", "acajap_CyB_JD"))

The following query will the return "materialSampleID" and "bcid" columns for all samples.

df <- queryMetadata('Sample', source=list("materialSampleID", "bcid"))

The following query will the return "materialSampleID", "bcid" and "eventID" columns for all samples and "eventID" and "locality" for all events related to the samples.

df <- queryMetadata('Sample', select=list("Event"), source=list("materialSampleID", "bcid", "eventID", "Event.eventID", "Event.locality"))

The following query will the return "materialSampleID" and "bcid" columns for all samples where a full text search matches "Chordata"

df <- queryMetadata('Sample', source=list("materialSampleID", "bcid"), query="Chordata")

The following query will the return "materialSampleID" and "bcid" columns for the samples in "acaach_CyB_JD" expeditions where "yearCollected" = 2008

df <- queryMetadata('Sample', projects=list(1), expeditions=list("acaach_CyB_JD"), source=list("materialSampleID", "bcid"), query="yearCollected=2008")

The following query will the return all fastqMetadata and related tissues, samples, and events which have an SRA (bioSample) accession number attached.

df <- queryMetadata("fastqMetadata", select=list("Event", "Sample", "Tissue"), query="_exists_:bioSample")

The following will fetch "CYB" fasta sequences and return a DNABin

fasta <- queryFasta('CYB')

The following will fetch "CYB" fasta sequences for the expeditions "acaach_CyB_JD" and "acajap_CyB_JD" collected after 2007 and return a DNABin

fasta <- queryFasta('CYB', projects=list(1), expeditions=list("acaach_CyB_JD", "acajap_CyB_JD"), query="yearCollected >= 2008")

You can fetch a list of the current fasta marker types:

markers <- listMarkers()

News

geomedb 1.0

This is a major release, which updates the package to work with the latest GeOMe changes.

  • queryMetadata:
    • query across multiple project & all data in GeOMe
    • query syntax has changed and now resenbles SQL
    • query results are returned for each entity. No longer a flat table representation

Reference manual

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install.packages("geomedb")

1.0.0 by RJ Ewing, 2 months ago


http://www.geome-db.org, https://github.com/biocodellc/fimsR-access


Report a bug at https://github.com/biocodellc/fimsR-access/issues


Browse source code at https://github.com/cran/geomedb


Authors: RJ Ewing


Documentation:   PDF Manual  


GPL-3 license


Imports ape, httr, jsonlite, data.table

Depends on utils


See at CRAN