README.md

PROXI Schemas

The HUPO-PSI Consortium defines community standards for data representation in proteomics to facilitate data comparision, exchange and verification.

The Proteomics eXpression Interface is a suite of integrated APIs each targeting a different aspect of exchanging proteomics information between ProteomeXchange data partners and consumers.

Here, all the api running can be hit: http://proteomecentral.proteomexchange.org/PROXI.php

Structure of the Repository

• meetings: Contains all the meeting discussions around the API.
• specs: Specifications folder including:
  • The swagger.yaml file contains the current definition of the API.
  • proxi-specifications.adoc : Ansible document definition, with examplesm, notations around the API.
  • proxi-specifications.pdf : PDF document definition, with examplesm, notations around the API.

Current implementations

PRIDE Repository

• Get dataset: http://wwwdev.ebi.ac.uk/pride/proxi/archive/datasets/PXD005011

• Search Datasets: http://wwwdev.ebi.ac.uk/pride/proxi/archive/datasets?pageSize=100&pageNumber=1&resultType=Full

Massive Repository

• Get Dataset: http://ccms-internal.ucsd.edu/ProteoSAFe/proxi/datasets?resultType=full&accession=PXD000561

• Datasets by contact: http://ccms-internal.ucsd.edu/ProteoSAFe/proxi/datasets?resultType=compact&contact=Pandey&pageSize=1

• Datasets by publication: http://ccms-internal.ucsd.edu/ProteoSAFe/proxi/datasets?resultType=compact&publication=draft%20map&pageSize=1

• Datasets by species: http://ccms-internal.ucsd.edu/ProteoSAFe/proxi/datasets?resultType=compact&species=mus

• Search Datasets Mod (modification=iTRAQ): http://ccms-internal.ucsd.edu/ProteoSAFe/proxi/datasets?resultType=compact&modification=iTRAQ

jPOST Repository

• List and search Datasets

  • https://repository.jpostdb.org/proxi/datasets
  • https://repository.jpostdb.org/proxi/datasets?resultType=full&pageSize=5
  • https://repository.jpostdb.org/proxi/datasets?contact=Ishihama
  • https://repository.jpostdb.org/proxi/datasets?species=rat
  • https://repository.jpostdb.org/proxi/datasets?species=rat,mus
  • https://repository.jpostdb.org/proxi/datasets?modification=iTRAQ
  • https://repository.jpostdb.org/proxi/datasets?instrument=Fusion
  • https://repository.jpostdb.org/proxi/datasets?publication=cancer
  • https://repository.jpostdb.org/proxi/datasets?accession=PXD005159
  • https://repository.jpostdb.org/proxi/datasets?accession=JPST000200
  • https://repository.jpostdb.org/proxi/datasets?search=colorectal

• Get Dataset

  • https://repository.jpostdb.org/proxi/datasets/JPST000200
  • https://repository.jpostdb.org/proxi/datasets/PXD005159

Contributing

The ProXI API is an open source project, feel free to contribute following the guidelines