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Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

Overview of attention for article published in BMC Bioinformatics, April 2018
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (58th percentile)
  • Good Attention Score compared to outputs of the same age and source (75th percentile)

Mentioned by

8 tweeters


28 Dimensions

Readers on

28 Mendeley
2 CiteULike
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Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions
Published in
BMC Bioinformatics, April 2018
DOI 10.1186/s12859-018-2118-1
Pubmed ID

M. Sivade, D. Alonso-López, M. Ammari, G. Bradley, N. H. Campbell, A. Ceol, G. Cesareni, C. Combe, J. De Las Rivas, N. del-Toro, J. Heimbach, H. Hermjakob, I. Jurisica, M. Koch, L. Licata, R. C. Lovering, D. J. Lynn, B. H. M. Meldal, G. Micklem, S. Panni, P. Porras, S. Ricard-Blum, B. Roechert, L. Salwinski, A. Shrivastava, J. Sullivan, N. Thierry-Mieg, Y. Yehudi, K. Van Roey, S. Orchard


Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.

Twitter Demographics

The data shown below were collected from the profiles of 8 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 28 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 28 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 10 36%
Student > Ph. D. Student 5 18%
Professor 4 14%
Student > Master 2 7%
Student > Doctoral Student 1 4%
Other 1 4%
Unknown 5 18%
Readers by discipline Count As %
Agricultural and Biological Sciences 10 36%
Biochemistry, Genetics and Molecular Biology 6 21%
Computer Science 5 18%
Pharmacology, Toxicology and Pharmaceutical Science 1 4%
Immunology and Microbiology 1 4%
Other 0 0%
Unknown 5 18%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 30 October 2018.
All research outputs
of 13,715,693 outputs
Outputs from BMC Bioinformatics
of 5,103 outputs
Outputs of similar age
of 272,831 outputs
Outputs of similar age from BMC Bioinformatics
of 24 outputs
Altmetric has tracked 13,715,693 research outputs across all sources so far. This one is in the 48th percentile – i.e., 48% of other outputs scored the same or lower than it.
So far Altmetric has tracked 5,103 research outputs from this source. They receive a mean Attention Score of 4.9. This one has gotten more attention than average, scoring higher than 51% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 272,831 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 58% of its contemporaries.
We're also able to compare this research output to 24 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 75% of its contemporaries.