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Challenges for glycomics repositories

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Logo of Beilstein-Institut zur Förderung der Chemischen WissenschaftenBeilstein-Institut zur Förderung der Chemischen Wissenschaften
 Packer, Nicolle H.

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Challenges for glycomics repositories
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Abstract
Glycomics data are generated by a variety of methods and techniques, for example, mass-spectrometry analysis of cell-surface polysaccharides, and the analysis of microbial biosynthesis pathways. These data are then stored in databases that are often neither comprehensive, nor interconnected. The current situation and perspectives for improvements are discussed in this video. Nicolle H. Packer is a Professor of Functional Proteomics at the Department of Chemistry & Biomolecular Sciences, Macquarie University, Sydney, Australia. Her research is focused on the investigation of the post-translational modification of proteins by sugars. In particular, her projects encompass the role of glycosylation in innate immune systems, and cancer glycomics. She is also interested in the development of separation technologies and informatics for the improved analysis of glycoproteins.
Keywords
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Glykobiologie
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Computer animation
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Breed standardCollectingGlykobiologieWursthülleMan pageMeeting/Interview
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GesundheitsstörungSea levelMeeting/Interview
Transcript: English(auto-generated)
00:22
It comes down obviously to people, it comes down to funding, it comes down to continuity and unfortunately over the years there have been many attempts at making these databases public and then they run out of steam because they run out of funding, they run out of permanence,
00:40
that to me is a major shortcoming. It happened in genomics, it happened in proteomics but until they could get continuous funding in some country making a commitment to maintaining this funding agency they also had similar difficulties to the ones we're having in glycomics.
01:06
It's probably inevitable in the early days of any field because everyone does their own thing but I think in this field we're up to the stage of amalgamating or bringing these things together and unifying them in one place, one accessible place, not necessarily physically on
01:21
the same place but virtually on the same place so that they're accessible and linked together across the whole. Well there's no reason why we can't do that now. I don't see any problem with it. I'm not a bioinformatician but according to my people that I work with it's
01:47
eminently possible to do that now. Clearly yes, the ultimate picture is to link them all
02:00
and get them all talking together. They have to be quality. To me the absolute essential part of any database effort is to keep the quality up, to make sure that what we look at is real and not just a collection of dumped data so the standards are essential.
02:23
Curation of literature would be one. Then for every technology which is used to acquire data to link to these structures, each technology would need its own standards to be developed based on what experimentalists demand of themselves in the laboratory. Absolutely,
02:50
within limits. I don't think we need to put every little bit of data on because to get creative scientists to do exactly the same thing is often quite difficult. But in terms of
03:03
technique, yes, I think we should record the details at that level.