New xref term: complex fragment

[lukasz99]

Hello, a relatively recent cryo-EM technique called focused refinement (see, eg PMID: 29856314, https://elifesciences.org/articles/36861) results in structures reported as collections of PDB files - one (or more) of them models entire complex but a number of additional ones correspond to individually refined (but otherwise not autonomous) subfragments. All of these should be entered as cross-references but 'identity' as cross-reference type does not seem particularly appropriate - the structures do not exist on their own but correspond to fragments of bigger structures.
So what about adding a new 'complex fragment' cross-reference type to use in such cases ?
it would be used for pdbs that do not correspond to complete complexes.

[pporrasebi]

We have 'subset' (MI:2179, synonym 'part of'), defined as 'Reference to the corresponding object in another database. It implies the object is part of a cross-referenced entity (usually a complex).'

Would this do? I would say it fits.

[lukasz99]

On 10/28/19 9:58 AM, Pablo Porras wrote:

We have 'subset' (MI:2179, synonym 'part of'), defined as 'Reference to the corresponding object in another database. It implies the object is part of a cross-referenced entity (usually a complex).'

Would this do? I would say it fits.

which way does it go ? is the referenced object 'part of' the one that the xref is hanging off or does it go the other way ? is the pdb part of the interaction or is the interaction part of pdb ?

lukasz

--

Lukasz Salwinski PHONE: 310-825-1402 UCLA-DOE Institute FAX: 310-206-3914 UCLA, Los Angeles EMAIL: lukasz@mbi.ucla.edu

[pporrasebi]

The pdb is part of the interaction: the xref would hang on an interaction/complex and refer to a PDB entry that represents part of it. We have been using it on the Complex Portal, here's an example: https://www.ebi.ac.uk/complexportal/complex/CPX-152. Go to the structures section and click through the different structures to see how they only represent part of the complex.

[lukasz99]

On 10/28/19 10:31 AM, Pablo Porras wrote:

The pdb is part of the interaction: the xref would hang on an interaction/complex and refer to a PDB entry that represents part of it. We have been using it on the Complex Portal, here's an example: https://www.ebi.ac.uk/complexportal/complex/CPX-152. Go to the structures section and click through the different structures to see how they only represent part of the complex.

so, I'd guess. then it's ok. lukasz

--

Lukasz Salwinski PHONE: 310-825-1402 UCLA-DOE Institute FAX: 310-206-3914 UCLA, Los Angeles EMAIL: lukasz@mbi.ucla.edu

[pporrasebi]

OK, closing the issue, then.