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MICommunity / psidev

@Deprecated please use https://github.com/HUPO-PSI Code exported from http://sourceforge.net/p/psidev/cvs/
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additional interaction type terms: indirect and unknown #45

Open SourceForge-exporter opened 18 years ago

SourceForge-exporter commented 18 years ago

Hello, Please could "indirect" and "unknown" be added as "interaction type"s in the controlled_vocab.? (I did email this around a couple of months ago, so apologies if this has already been addressed and I have missed an email).

http://psidev.sourceforge.net/mi/rel25/data/psi- mi25.obo

From literature or data vendors one can not always make a "confident" call on whether an interaction is is direct or indirect, so that is why unknown is useful. Having some general terms like direct, indirect and unknown helps people, without having to create yet another attribute. "direct interaction" (MI:0407)

We have been using them but just used MI:0190 (interaction type) with our additional terms. Even if it will only be in a future controlled_vocab. listing that is fine, but it would be useful to know what the MI:numbers will be.

Alternatively, could there be a field for directionality of interactions? so that it is quick to see whether the evidence points to an interaction being direct, indirect or unknown(unsubstantiated).

Thanks a lot, Peter Bioformatics Science and Technology GSK

Reported by: *anonymous

SourceForge-exporter commented 18 years ago

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Although we perfectly understand the need of directionality distinction we do not see use case for the term 'indirect interaction'. When a interaction is analyzed if there is not enough evidence to state that the interaction is direct we use the interaction type 'physical interaction' MI:0218. This term covers your 'unknown' status and is defined as "Interaction among molecules that can be direct or indirect". When proteins are purified or the overall experimental setting is appropriate the interactions are promoted to 'direct'. I do not see cases when you can assume an interaction is 'indirect'. In my opinion an interaction between protein A and protein B is prove to be indirect only when a 'bridging' protein C is observed/identified (in this case the interactions A-C and B-C would be reported as 'direct' interactions) otherwise it remains an interaction with 'unknown directionality' thus a physical interaction in PSI-MI terms. A classical example could be the TAP complexes that certainly contain a mixture of direct and indirect interactions but are annotated as 'physical interaction' as the data do not provide such detailed information. If you do not agree, please send me examples of assays that provide interaction you can assume to be 'indirect' or papers that contains interactions you would annotate as 'indirect'.

For now consider the following mapping for interaction data from public databases: -direct : 'direct interaction' MI:0407 and all direct interaction children terms -unknown : 'physical interaction' MI:0218, 'colocalization' MI:0403, 'genetic interaction' MI:0208 and all genetic interaction children terms -indirect interaction : Non Available

Luisa

Original comment by: luisa_montecchi