Open Letter to the Steering Committee of SeaLice 2018

Imagine any major Drosophila conference some years  ago. Is it thinkable that The FlyBase Consortium submitts an abstract on advance and updates of FlyBase and then got met with a poster presentation?

Unfortunately, the descision to assign a poster presentation to the only online-resource dedicated to sea lice genomics, is in line with a perceived trend of marginalizing proper bioinformatics and data-base resources within the sea lice community. There are already already too few people within sea alice research working on providing tools and resources, and this descision does not make it any easier to recruit skilled bioinformaticians willing to build up some infrastructure that purely serves this field. It is further a very unfortunate perspective, that seemingly within a four-days conference, only three hours are assigned to molecular biology topics.

For this reason, I have decided to make our response open on LiceBase to put the finger at this important problem. 

On Aug 17, 2018, at 10:22 AM, Michael Dondrup <michael.dondrup@ii.uib.no> wrote:

To the Members of the Steering Committee of the Sea Lice Conference 2018,

 

We would like to thank you for accepting of our abstract “LICEBASE - a genome centric organism database for sea lice and related organisms” for presentation at the Sea Lice 2018 conference. However, and with all due respect, we have to protest against the assignment to a Poster presentation because we firmly believe that this decision does not reflect appropriately upon the relevance and merits of our contribution for the global sea lice research community. LiceBase is a unique resource. As to the best of our knowledge, there is no comparable database within the sea lice community. LiceBase provides the community with an updated and high-quality annotation of one of the two major species with commercial impact on global aquaculture. It also provides accessto over 150 RNAi experiments, providing an effective link of gene, annotation, phenotype and associated publication, which, given the complexity of RNAiexperiments on the host, results in approximately 2-3 years of net research value spent on generating these data.

Links to other species’ transcriptomes and genomes are present through our Blast interface. Tigriopus kingsejongensis is a recently sequenced genome of a free-living copepod that we have imported into LiceBase, as there was no other genome browser available for this genome. Orthologous genes between Trigriopus and Lepeophtheirus have been detected and linked, allowing researchers to better detect genes specific to e.g. parasitic life-style. Furthermore, through the genome browser, we provide access to almost 100 transcriptomics datasets and other data tracks, including unpublished data. Similar data-bases have been existing for a long time for other model organisms, such as  FlyBase http://flybase.org/ or WormBase https://wormbase.org/, or http://www.genomernai.org/ for RNA-i knock-down data. Model organism databases have been instrumental to building the research community for their respective organism around them, gathering researchers from all over the globe. FlyBase, as an example has possibly shaped the way we view modelorganisms today more than any other resource, since it was created over 25 years ago. We hope that LiceBase will be appreciated by the sea lice community in a similar fashion as FlyBase was by the Drosophila community. LiceBase has been up and running since 2014, since then we have added a huge amount of new features, new data and other important updates, we would like the community to know about. 

 

We certainly wish to invite more researchers to contribute new data, and would in particular welcome data from Caligus species, which as to the best of our knowledge does not have a scaffolded genome and few associated RNAi experiments yet.  At SLRC, we are dedicated to open science, and therefore content in LiceBase is made freely and openly available, with only very few exceptions for the newest unpublished experiments. What is more, our contribution is trying to alleviate the fact that genomics resources for any other arthropod group than insects are still very sparse. We would further like to stress the fact that future funding for LiceBase has been secured through the Norwegian Elixir Node https://www.elixir-europe.org/about-us/who-we-are/nodes/norway and continuation of SLRC is supported by the University of Bergen.

LiceBase is an international deliverable from the Norwegian Elixir node.

 

Computational genomics, bioinformatics on-line tools and databases play an ever large role in sea lice research as precedented by research in human medicine and other model organisms. These tools have an enormous potential in drug and target discovery and discovery of novel gene functions. They do this by giving scientists access to a wealth of knowledge about genes, genomes, proteins, phenotypes, and high-throughput data. In the light of the undeniable impact that computational tools and databases have in the field of biomedical research, the level of appreciation that is expressed in this decision about one of the few on-line resources dedicated to sea lice seems particularly unjustified. 

 

We hope that the committee could reconsider their decision and assign our contribution to an oral presentation slot, to make the community aware of the existence, recent updates, and novel possibilities provided by LiceBase. We are looking forward to hearing from you and thank you in advance for your consideration.

 

Yours truly,

 

Michael Dondrup

Senior Researcher

Sea Lice Research Centre

Department of Informatics

University of Bergen

Thormøhlensgate 55, N-5008 Bergen, 

Norway