New features May 2018:


Content overview bars

Glycan structure lists (in search results or as references in entry pages) now include a summary of the entry content. In these overview bars users can easily see what kind of information is available for the entry, as e.g. for glycan structure #298:

Structure entry #298: Man-9 N-glycan linked to Asn

a-D-Manp-(1-2)-a-D-Manp-(1-6)+ | a-D-Manp-(1-6)+ | | a-D-Manp-(1-2)-a-D-Manp-(1-3)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn | a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+
1H: 1 : 10  : 63  Taxons: 11

From the content overview, you can see that (as of May 13th, 2018) for this entry there is a 3D structure model and 1 proton NMR spectrum available, 10 PDB entries and 63 literature publications are referenced, and 11 taxons for which the structure has been reported are stored in the database, but no GlycoMap is present for this structure. This information helps users to find the data they are looking for in a list of glycan structure entries without having to click each individual entry. Furthermore, the content summary boxes are linked with the corresponding section of the glycan structure entry.

Titles and keywords for glycan structure entries

We introduced the possibility to add titles to glycan structure entries, which are displayed on top of the entry pages and in glycan structure lists (see the example of Man-9 above). This shall make it easier for users to assign glycan structures to well-known names used in the literature. Keywords can also be assigned to for use in queries (see below). Of course the assignment of titles and keywords is mostly a manual process, and not for all glycans senseful titles can easily be created. Therefore, this feature will be available for a subset of entries only. We plan to provide an option for users to suggest titles, keywords (and other information such as literature references as well) in the future.

Individual pages for literature references and PDB entries

So far, literature and PDB entries in Glycosciences.DB have just been shown as lists of referenced glycan structure entries with very little further information. Now, each entry has a separate page, which summarizes all available information. This makes it easiser to link to these entries from resources outside Glycosciences.DB as well.

Connection of literature references and glycan structures via PDB entries

Most literature references in Glycosciences.DB that have glycan structures assigned have been imported from CarbBank (and thus are rather old now). The main source of new information in recent years has been the Protein Data Bank (PDB). Glycosciences.DB now also imports literature references from those PDB entries that are linked to glycan structure entries. However, these publications are not linked to the glycan structures directly. This is done because the references often contain information on the glycans that are present in the PDB entries, but that is not always the case. Especially when just small N-glycan fragments are present, and the glycans are not the main subject of the study, there might be no further information than "glycans have been detected" in the publications. Nevertheless, literature references imported from the PDB can be valuable sources for glycoscientists as well. To allow users to distinguish between manually assigned publications and those that are linked to the glycans via PDB entries, the latter are listed separately both in glycan structure entries (where there are sections entitled "Literature references" and "Literature references from PDB entries") and in the bibliography entries ("Glycan structures" vs. "Glycan structures from referenced PDB entries").

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