Genex.pm

# The Genex.pm Distribution

Welcome to Genex.pm, I hope you enjoy your visit.

# Introduction

Genex.pm is a Perl module to enable bioinformatics researchers to access a GeneX gene expression database (DB) via Perl. It provides an application programmers interface (API) consisting of table classes and utility classes, and it also comes with a tutorial and a number of example scripts to help researchers write their own tools.

# Table Classes

The majority of the modules included in the Genex.pm distribution provide access to a single table in the Genex DB. The purpose of the table classes is to simplify accessing information from the DB by shielding many of the DB's underlying details from the developer.

The table classes can be divided into three logical groups:

- Main data table classes
  - AL_Spots.pm,
  - AM_Group.pm,
  - AM_Spots.pm,
  - ArrayLayout.pm,
  - ArrayMeasurement.pm,
  - CanonicalSequenceFeature.pm,
  - Chromosome.pm,
  - Citation.pm,
  - Contact.pm,
  - ContactType.pm,
  - ExperimentFactors.pm,
  - ExperimentSet.pm,
  - ExternalDatabase.pm,
  - GroupSec.pm,
  - Protocol.pm,
  - Sample.pm,
  - Scanner.pm,
  - Software.pm,
  - Species.pm,
  - Spotter.pm,
  - TreatmentLevel.pm,
  - Treatment_AMs.pm,
  - UserCanonicalLink.pm,
  - UserSec.pm,
  - UserSequenceFeature.pm,
- Linking table classes
  - AM_FactorValues.pm,
  - AM_SuspectSpots.pm,
  - BlastHits.pm,
  - CSF_ExternalDBLink.pm,
  - CitationLink.pm,
  - GroupLink.pm,
  - HotSpots.pm,
  - RelatedCSF.pm,
  - SampleProtocols.pm,
  - SpotLink.pm,
  - TL_FactorValues.pm,
  - USF_ExternalDBLink.pm,
- Controlled vocabulary table classes
  - ALS_SpotType.pm,
  - AL_Coating.pm,
  - AL_DefaultSpotConcUnits.pm,
  - AL_IdentifierCode.pm,
  - AL_Medium.pm,
  - AL_TechnologyType.pm,
  - AM_EquationType.pm,
  - AM_SpotMeasurementUnits.pm,
  - AM_Type.pm,
  - CSF_Type.pm,
  - ControlledVocab.pm,
  - EF_MajorCategory.pm,
  - EF_MinorCategory.pm,
  - ES_QuantitySeriesType.pm,
  - ES_TreatmentType.pm,
  - HS_ThresholdType.pm,
  - PRT_Type.pm,
  - SCN_ModelDescription.pm,
  - SMP_AgeUnits.pm,
  - SMP_DevelopmentStageName.pm,
  - SMP_DevelopmentStageUnits.pm,
  - SMP_GeneticStatus.pm,
  - SMP_OrganType.pm,
  - SMP_OrganismIntactness.pm,
  - SMP_PrimaryCellType.pm,
  - SMP_SexMatingType.pm,
  - SMP_TissueType.pm,
  - SPC_CellStructure.pm,
  - SPC_GeneralClassification.pm,
  - SPC_Generalclassification.pm,
  - SPT_ModelDescription.pm,
  - SPT_ModelName.pm,
  - SW_Name.pm,
  - SW_Type.pm,
  - USF_Type.pm,

# Utility Classes

Many of the mundane needs of developers working with a Genex DB have been simplified by adding commonly used functions to helper modules.

See the individual modules for more details:

- Genex.pm itself, which contains helper functions for connecting to a GeneX DB, and
- DBUtils.pm, which contains helper functions for retrieving and storing data in a GeneX DB, and
- HTMLUtils.pm, which contains helper functions for converting information to HTML.
- XMLUtils.pm, which contains helper functions for converting information to XML.

### Author and Copyright

This module and its documentation were written by Jason E. Stewart (jes@ncgr.org), and all the material is copyright © 2000 the National Center for Genome Resources.