What does this database contain?

This database aims to assemble a comprehensive collection of structured phenotyping data from attempts to knock out Plasmodium genes. It is organised such that by searching for a gene in any species you can also see results for orthologous genes. You can see the number of phenotyped genes per species on our statistics page. Its development is described on Wellcome Open Research.

Data sources

Data for rodent malaria parasites shown in this database comes from the Rodent Malaria genetically modified parasites database (RMgmDB) or PlasmoGEM. Clicking on the Reference link on any of these phenotypes will take you to the RMgmDB or PlasmoGEM page for that disruption attempt, which will often contain more detailed phenotyping information.

Other data is curated by our users or administrators from the Plasmodium literature, primarily for P. falciparum, here the reference link will take you to the PubMed page for the publication in question, which will have further details on the experiments involved.

If citing this database, please remember that RMgmDB (described here and here) and PlasmoGEM constitute a large part of the dataset.

Genome data comes from GeneDB via PlasmoDB.

How do I add data?

It is easy to contribute data to PhenoPlasm, simply click the [+] button next to the Phenotypes heading. We are not a primary datasource, so please include a PubMed ID or other reference to the description of the experiment generating the phenotype.

Please prioriotise submitting any data on rodent malaria parasites to RMgmDB, from which it will ultimately be mirrored here.

How does orthology work?

Orthologs are genes in different species which have a common ancestor, e.g. PfAMA1 and PbAMA1. In general these are expected to have the same function in the various species, and so to have the same phenotype when knocked out. Because of this we display information from orthologs in other species when you search for a gene. These are displayed on the search page with semi-transparent icons so you know they represent orthologous results.

Where can I see the complete dataset?

We have a data dump of all phenotypes in the dataset. You can aso extract data from any search in CSV format. Details of the taxonomy used in CSV format are available here.

Who can I contact to amend this data?

Please email the curator if you spot any errors. If subsequent publications contradict previous results please add the data from them, as described above.