diArk Help pages

How to use diArk's search modules

Search in scientific   and common names

Browse taxonomies and model organisms

Select specific species groups

Search by author, year or title

Search by sequencing project

The database is searched using modules that can be combined in chains. There are five different modules each providing specific options: a module for the full-text search in all species names, a taxonomy search module, a module to select specific groups of species, a module to search sequencing project related data, and a publication search module. A search can consist of any combination of modules and their options. By adding further search modules the user can successively refine the search and narrow down the result list. For each module the resulting selection of species, projects and publications is shown, providing additional context. When a new module is added the options available are restricted by the selection from the previous modules. At any time, the search options for every module can be changed and modifications are propagated down the chain reapplying previous user actions.

Note: All species results will be listed under the reference scientific name (according to the NCBI taxonomy browser). Thus anamorphs will be listed under their teleomorph names (e.g. if you are searching for Fusarium verticillioides the main entry will be Gibberella moniliformis citing F. verticillioides as anamorph) and the same accounts for alternative scientific and common names.

Species Names search module

The full-text search module provides an autocompletion input field to search the list of scientific and common species names. The default setting is that all different subsets of species names are marked. You can use your mouse or keyboard to select a species from the autocompletion list but you have to press "enter" a second time to submit your selection.

Note: If you just enter a single letter you will get the list of all species starting with this letter, depending on your selection of scientific, alternative and/or other names.

Taxonomy search module

The taxonomy search module offers tables containing specific subsets like a selection of major taxa or a range of model organisms. Several different strains have been sequenced for some of the model organisms. Those are marked with exclamation mark icons. In addition, on mouse-over the species names the complete scientific strain names are given.

Note: If the dataset has been restricted by previous modules (e.g. the selection of a specific reference), excluded species and taxa are disabled in the tables and will not be shown in the taxonomic tree representation.

The taxonomy search module also provides a taxonomic tree representation for the selection of taxa and species. On top of the tree representation, there are two autocompletion input fields, one for taxa and one for species names. The species name input field accepts all different types of names, the scientific names, the alternatively used names, common names, and the anamorphs, while it selects the scientific reference name. After submission of the taxon/species name search, the taxonmy tree is reloaded with the selected taxon/species name opened.

Instead of searching for taxa or species names, taxa and species can be browsed and selected by expanding/collapsing and including/excluding subsections of the tree.

	Clicking the arrow-down icon will expand the tree by 1 taxon.
	Clicking the double arrow-down icon will expand the complete subtree. On mouse-over the icon the number of sub-taxa and species will be given.
	Clicking the arrow-up icon will collapse the subtree.

On mouse-over a species name an image of the species will be shown. Selecting a taxon will select the complete subtree and all species included. This will also select all taxa/species that are not shown based on restrictions in previous modules. The rationale is, that you might want to change your restrictions in a previous module but still want to keep your taxonomic selection. For example, if you restricted your search to genomic sequences in the projects module and selected the Arthropoda you will only see Arthropoda species with sequenced genomes. If you then change your selection in the projects module to also include the cDNA/EST projects, your species selection will automatically expand to include all Arthropoda for which genomic sequences and/or cDNA/EST data are available.

Note: Expanding the complete tree or major taxa (e.g. the Fungi/Metazoa group) will cause Firefox to take some time to render the updated view.

Species Groups search module

With the Species Groups search module specific subsets of species can be selected that do not necessarily correspond to certain taxa. We plan to expand this tool to show more general information about the species groups listed. These informations would include for example the rationle for the selection of the four Plasmodium falciparum strains for genomic sequencing. At the moment, only subsets of species can be selected.

Publication search module

The publications related to the species and sequencing projects can be searched in several ways. Full-text searches are provided for titles, authors and journals. In addition, the journal search input field is supplemented with an autocompletion function. Searches can be restricted by dates. By default, searches are unrestricted.

Note: Only by selecting the Publications search module, the species are already restricted to those whose genome or cDNA/EST data has been referenced in a publication.

Projects search module

The projects contain details concerning a specific sequencing effort, such as its type (genomic DNA or EST/cDNA) and a link to the web-page providing the primary data. Projects can be selected based on the sequence data available for the species. Thus, species might be selected for which only cDNA/EST data or only genomic data is available, or those for which both cDNA/EST and genomic data is available. The term completeness is intended to describe the coverage of the genome and the chance to find all homologs of the gene of interest. For detailed information have a look at the FAQ's pages. The completeness option offers the possibility to search for those species for which the chance to find all homologs (and complete genes) to the protein of interest is very high. The projects have been organized by references, a term we use for the large-scale sequencing centers (e.g. the DOE Joint Genome Insitute) or community species homepages (e.g. FlyBase). By choosing references it is possible to search for the ouput of a single or more sequencing centers. However, for many species, the sequence information is not available via a dedicated species home page but only via GenBank. Therefore the "GenBank" links (associated to the GenBank reference) of the species projects provide BLAST search forms including the corresponding database (some data is only available from the WGS, other from the EST database) and the corresponding species name.

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