W612 Nucleic Acids Research, 2012, Vol. 40, Web Server issue a programmatic way. In this section, we describe URLs syntax and provide some usage examples and details on how to access data. Understanding the CellBase web services API structure Biological information can be accessed easily using URLs. These URLs have been designed to be ﬂexible, neutral and scalable in future extensions, permitting the addition of new methods without altering the structure. The general syntax of CellBase URLs is as follows: ws.bioinfo.cipf.es/cellbase/rest/version/species/category /subcategory/id/resource?ﬁlters The ﬁrst part of the URL, ws.bioinfo.cipf.es/cellbase/ rest, refers to the host and is ﬁxed for all methods. The remainder part will vary depending on the user’s query. ‘Versions’ are numbered with the letter ‘v’ followed by a number (i.e. v1) or by the keyword ‘latest’ to access the current release. The ‘species’ ﬁeld can be speciﬁed using the three-letter code (hsa, mmu, rno, etc.) or the abbreviated format (hsapiens, mmusculus, rnorvegicus, etc.). Currently, biological information is available for 11 species, as described above. ‘Category’ ﬁeld aims to provide a general classiﬁcation for the input identiﬁer according to its nature. Four main categories are available: . ‘Genomic’, which makes reference to genomic coord- inates like regions, positions or variants. . ‘Feature’, involves all elements that have a deﬁned location on the genome and provides a comfortable way to retrieve cross references for an identiﬁer. . ‘Regulatory’, refers to all regulatory features, including interactions that involve TFs and microRNAs. . ‘Network’, makes reference to different types of networks and pathways, including the protein interactome, the regulatory network and Reactome. The ‘subcategory’ ﬁeld must indicate the type of the input identiﬁer (gene, transcript, region, pathway, etc.). Users can choose the most suitable one among the prede- ﬁned subcategories. ‘Id’ is the query parameter, the feature or term about which the user wants to retrieve the information. Users can query more than one identiﬁer using a comma separated list. The ‘resource’ ﬁeld refers to the information the user wants to obtain from the id ﬁeld. Depending on the category and the subcategory speciﬁed, different ‘resources’ are available. Resources must always be written in singular. Table 1 summarizes a representative selection of the available resources for each category and the corresponding subcategories. Identiﬁer types and formats for each subcategory are also described. Users can add ‘ﬁlters’ to the RESTful query after the question mark. Some of them can be applied to all queries, but some of them are speciﬁc for each subcategory. An example of the options that can be applied to all queries are the output format, coded as ‘of’, and the character used to separate columns in the resulting output, coded as ‘separator’. Additional web services have been designed to provide metadata about CellBase and web services themselves like retrieving information about the available species, genome assemblies or species codes. In addition, column headers and usage about subcategories have been added to provide an online help to users. Detailed and up-to-date information of currently available methods can be accessed by visiting the docu- mentation page at http://docs.bioinfo.cipf.es/projects/ cellbase/wiki. Examples of CellBase RESTful web services queries To provide a clarifying idea about what these web services are able to do, here we show some examples of usage. Example 1. To obtain the SNPs of a particular region (i.e. chromosome 16 from 3698105 to 3701105), we use the genomic category since the speciﬁed inputs are genomic coordinates: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/genomic/ region/16:3698105-3701105/snp Example 2. Retrieving all transcripts for a gene is straightforward using the feature category: http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/ gene/BRCA2/transcript Table 1. Summary of some of the main available categories and subcategories Category Genomic Feature Regulatory Network Subcategory Region Variant Position Gene Transcript Snp Exon Protein Id mirna_gene mirna_mature Tf Pathway Interactome Identiﬁer format chr:start-end chr:position:new allele chr:position All gene ID formats Ensembl or RefSeq ID dbSNP or Ensembl ID Ensembl ID UniProt or Ensembl ID All possible IDs miRBase gene ID miRBase mature ID TF or gene name none Reactome pathway name UniProt or Ensembl ID Resources gene, transcript, snp, sequence, reverse, tfbs, mirna_target, regulatory consequence_type gene, snp, mutation, functional info, sequence, transcript, tfbs, mirna_target, protein_feature, snp, mutation info, gene, sequence, exon info, consequence_type, population_frequency, phenotype, xref info, sequence, region, transcript info, gene, sequence, transcript, feature, xref, variant Xref info, gene, mirna_mature, target, disease info, gene, mirna_gene, target, disease info, tfbs, gene, protein, pwm List info, subpathway, element, gene, protein, image info, element, neighbourhood, adjacent, connected_component