ChlamBase: a curated model organism database for the Chlamydia research community

Abstract

The accelerating growth of genomic and proteomic information for Chlamydia species, coupled with unique biological aspects of these pathogens, necessitates bioinformatic tools and features that are not provided by major public databases. To meet these growing needs, we developed ChlamBase, a model organism database for Chlamydia that is built upon the WikiGenomes application framework, and Wikidata, a community-curated database. ChlamBase was designed to serve as a central access point for genomic and proteomic information for the Chlamydia research community. ChlamBase integrates information from numerous external databases, as well as important data extracted from the literature that are otherwise not available in structured formats that are easy to use. In addition, a key feature of ChlamBase is that it empowers users in the field to contribute new annotations and data as the field advances with continued discoveries. ChlamBase is freely and publicly available at chlambase.org.

Figure 1

The semantic data model within Wikidata for ChlamBase content. Nodes in this graph represent classes of Wikidata items that are used in ChlamBase, with the count of each item class in parentheses. Edges in the graph represent statements in Wikidata that relate two items, with the total edge count between item types shown in parentheses.

Figure 2

Overview of the ChlamBase gene page interface. (A) Search box to query the ChlamBase database for genes and keywords. (B) Log in button that redirects the user to a Wikimedia.org login for Wikidata account authorization and to allow the user to make edits or annotations using their credentials. (C) Display of the Chlamydia species and/or strain the current gene belongs to with strain-specific icons. (D) Key identifiers for the current gene, including gene name, gene symbol, locus tag and aliases. (E) Gene expression module showing the timing of expression (life cycle period or constitutive), expression in either chlamydial cell form (elementary body or reticulate body) and a cell localization diagram. (F) Mutant annotations produced by chemical, transposon, intron and recombination mutagenesis. (G) Annotation modules contain integrated and user-curated data for Gene Product, Ortholog(s), Ortholog Alignments, Expression Timing, Gene Ontology Annotations, Operon, InterPro Domains, Enzyme functions, Mutants, Protein Interactions and relevant Publications. All modules are loaded in expanded view upon page loading; module expansion and/or collapsing can be manually toggled by the user. (H) The gene page footer contains links to corresponding reference entries in NCBI and Wikidata, related publications identified by locus tag and species co-mention in the text and a link to the revision history in Wikidata.

Figure 3

Ortholog and Ortholog Alignment modules. (A) Computationally derived orthologous genes from other Chlamydia genes in ChlamBase are displayed in a table along with the current gene. The table displays NCBI taxonomy IDs for orthologous genes, their locus tags (clicking on them redirects the user to those genes) and binary displays (by green or gray dots) of whether annotations are available in current/ortholog genes for Gene Expression, InterPro Domains, Host–Pathogen Interactions, Gene Ontology Annotations, Operons and Mutants. References open up Wikidata pages for that gene. (B) Ortholog Alignment tool uses the MSAViewer widget (19) to display DNA or amino acid alignments for orthologous genes or proteins, toggle species/strains to use for alignments and download aligned sequence data in a FASTA-compatible window.

Figure 4

Chlamydia mutants module. Sample display of mutants for CTL0374 IncA, containing five mutant strains generated by chemical mutagenesis. The tabular view of chemical mutant strains displays strain names, genomic positions of mutations, the L2 reference and variant bases, SNV type, effects of each mutation on the respective amino acid sequences and a link to the publication reference. `Add an annotation’ opens a form for the submission of new mutant entries to ChlamBase.

Figure 5

Host–Pathogen Interactions module. Sample information for CTL0260 IncV, containing a host protein found to interact with IncV, its corresponding gene symbols, host species, the determination methods used for this evidence and links to the publication references.

Figure 6

Annotation submission forms for ChlamBase. The GO form prompts the user to submit information for (A) GO term, typeahead enabled and the method used for determination (i.e. inferred from experiment and inferred from sequence orthology); (B) the ability to map the GO annotation to orthologous strains, and the PubMed reference used as the experimental basis for this annotation. (C) Mutant annotation form asks the user to submit information for: (i) mutant strain name, (ii) mutation type (i.e. chemical mutagenesis or transposon mutagenesis) and (iii) the PubMed or FigShare reference that serves as the evidence for the annotation. Additional mutant information is available for entry depending on the mutation type chosen by the user.