Help Menu for Integrated Genetic Map Data Web Services

• Overview

  Research activities over the past several years have dramatically increased the volume of high-density genetic map data that is available from multiple databases via a range of hypertext markup language (HTML) based Web interface tools.  However, variations in database systems, architectures and bioinformatic tool formats can make data integration problematic. Web services offer a remedy by providing bioinformatic tool and pipeline developers with access to the data in a well defined format.  Web services are designed to provide reusability and interoperability between diverse applications. They are reusable software components that are created once and can be used by many applications. Web services are different than searchable web interfaces. Web interfaces are designed for interactive search and require human intervention; they fall short for automatic data retrieval.    The reason is that web pages use hypertext markup language that is mainly used for content display. On the other hand, the underlying format of web services is extensible markup language (XML) which is well suitable for hierarchical data. Since XML is the de facto universal data format for data exchange between platform independent applications, web services open the opportunity for the easy integration of heterogeneous systems. A web service written in Java can be invoked by a program written in Perl, or vise versa. Web services enable  bioinformaticians to collaborate more effectively.Using our primary web services you can browse linkage groups and display genetic map objects in the context of map locations. The following instructions show you how to accomplish these tasks in detail.

  1. Get metadata such as species, map name and map identification.
  2. Get chromosome/linkage groups for a given map id.
  3. Get maximum lentgh of a chromosome/linkage group.
  4. Get probes for a given map region.
  5. Get BACs for a given map region.
  6. Get polymorphisms for a given map region.
  7. Get map locations for a given objects.
  
  

  Note:
  Chromosome numbers, based on the recently developed identification and nomenclature of Kim et al. (2004), have been added to the sorghum linkage group labels.

  Kim, J., Klein, P.E., Klein, R.R., Price, H.J., Mullet, J.E., Stelly, D.M. (2004) Chromosome identification and nomenclature of Sorghum bicolor. Genetics: Published Articles Ahead of Print. Genetics.104.035980.
  
  

• Get metadata such as species, map name and map identification.

  Currently, map data is collected in our relational database for three species. To view map data, first get the species, map name and map identifcation.

• Get maximum length of a chromosome/linkage group

  The map objects are organized alongside the map based on their physical locations. To explore the map objects, one needs to know the maximum length of a given chromosome/linkage group.

• Get chromosome/linkage groups for a given map id.

  The service provides names of chromosome/linkage groups for a map.

• Get probes located within a specified map region.

  There are three types of map objects: probes, bacs, and polymorphisms. This service allows users to get probes and locations for a specified map region. The region is specified by setting the location and range parameters and all objects between (location-range) and (location + range) are returned. To get all probes located on a chromosome/linkage group, one can set the range parameter equal to -1.

• Get BACs located within a specified map region.

  There are three types of map objects: probes, bacs, and polymorphisms. This service allows users to get BAC contigs and locations for a specified map region. The region is specified by setting the location and range parameters and all objects between (location-range) and (location + range) are returned. To get all BAC contigs located on a chromosome/linkage group, one can set the range parameter equal to -1.

• Get polymorphisms located within a specified region.

  There are three types of map objects: probes, bacs, and polymorphisms. This service allows users to get polymorphism related data and locations for a specified map region. The region is specified by setting the location and range parameters and the Web service returns data for all objects between (location-range) and (location + range). To get data for all polymorphisms located on a chromosome/linkage group, one can set the range parameter equal to -1.   The following table shows the polymorphism related data items that are returned:

Tag	Data item
PROBE_NAME	associated probe name
LOCATION	location
DIV_REF_STOCK_ID	Institute of Genetic Diversity Id.
ALLELE_COUNT	allele count
NUM_POLY_SITES	total number of polymorphic sites
NUM_SUBST_SITES	number of substitution sites
NUM_INDEL_SITES	number of indel related sites
NUM_INDELS	number of indels
POLY_SPREAD	sequence spread or the distance, in nucleotide bases, between the most 3' and 5' polymorphic sites
GB_POPSET	GenBank PopSet Id.
GB_LOCUS	GenBank locus Id.

•   Get map locations for a given object

  It is possible for a single object to be associated (mapped/anchored) with more than one location on a single or multiple chromosome/linkage groups. This service returns a list of the loctions and chromosome/linkages groups for a given map object.

•   Get probe locations for a given GenBANK accession

  It is possible for a single probe to be mapped to more than one location on a single or multiple chromosome/linkage group(s). This service returns a list that includes the the probe name, map name, chromosome/linkage group(s) and location(s) for a given mapped probe's accession Id.