If you are installing a subset of the standard Ensembl species, you can leave the plugins as-is and your home page will be generated automatically.
If, however, you are adding species from taxa not found in Ensembl, e.g. plants or bacteria, you will need to create the appropriate files in your site plugin.
For a site with few species, it is usually sufficient to provide a list of static links, or
a simple list can be auto-generated using the information stored in SpeciesDefs. See
EnsEMBL::Web::Document::HTML::SpeciesList for sample code.
If your site has a lot of species, you may wish to group these in a similar way to Ensembl. To do this, you need taxonomy data in the 'meta' table of your core database. The standard format is for the taxa to be listed in ascending order when ordered by meta_id, e.g.
mysql> select * from meta where meta_key = 'species.classification' order by meta_id; +---------+------------------------+------------------+ | meta_id | meta_key | meta_value | +---------+------------------------+------------------+ | 1039 | species.classification | sapiens | | 1040 | species.classification | Homo | | 1041 | species.classification | Hominidae | | 1042 | species.classification | Catarrhini | | 1043 | species.classification | Haplorrhini | | 1044 | species.classification | Primates | | 1045 | species.classification | Euarchontoglires | | 1046 | species.classification | Eutheria | | 1047 | species.classification | Mammalia | | 1048 | species.classification | Euteleostomi | | 1049 | species.classification | Vertebrata | | 1050 | species.classification | Craniata | | 1051 | species.classification | Chordata | | 1052 | species.classification | Metazoa | | 1053 | species.classification | Eukaryota | +---------+------------------------+------------------+
When provided with a list of taxa, SpeciesDefs will compare the two in order to classify your species into groups.
The next step is therefore to identify the taxa that correspond to the groups you want. Ideally you want about 2-7 species in each group (the normal range for human short-term memory to handle). In Ensembl, we have many different mammal species, some other vertebrates, and a few non-vertebrates. We have thus divided our species as follows:
* Although these are distinct groups, they have few representative genomes at present, so we list them together
Once you have decided how to group your species, you need to sketch a taxonomic tree that includes the identifying nodes. In the diagram below, the highlighted taxa are the ones that will be needed to separate species into the required groups.
Finally you will need to set up your [plugin]/conf/ini-files/DEFAULTS.ini to contain the groups you wish to select and the corresponding labels. The order of the groups must follow your taxonomic tree from bottom to top:
TAXON_ORDER = [Primates Euarchontoglires Laurasiatheria Afrotheria Xenarthra Metatheria Monotremata Aves Sauropsida Amphibia Euteleostomi Chordata Eukaryota]
If you want any of these taxa to be grouped together, or to use labels other than their scientific name, you also need a hash of labels:
[TAXON_LABEL] Euarchontoglires = Rodents etc. Metatheria = Marsupials & Monotremes Monotremata = Marsupials & Monotremes Aves = Birds Sauropsida = Reptiles & Amphibians Amphibia = Reptiles & Amphibians Euteleostomi = Fish Chordata = Other chordates Eukaryota = Other eukaryotes
Note that by setting the same group label for different taxa, we can combine taxonomic groups that are in different branches of the taxonomic tree
A few things that could potentially cause problems are:
[TAXON_LABEL]
# Accept defaults
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