Results of the Survey on Needs for Data Standardisation and Databases in Molecular Biophysics

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Are We “FAIR” in Molecular Biophysics

The field of molecular biophysics encompasses several dozen techniques, with new methodologies appearing almost annually. Given this range of alternative methods for accomplishing similar research goals there is a high degree of variation in the level of usage of each method in the community. Most of the methods lack any accepted standards of data records and/or publicly accessible repositories or databases, and there are certainly no shared standards for reporting raw data or derived results. Researchers utilizing these techniques approach them for their research projects with varying expectations, levels of expertise, and have different personal needs for data archival. The principles of FAIR data management are also not generally known or accepted. The community of scientists utilizing these methods does not belong to one particular field of science or industry and includes specialists in biology, physics, chemistry, medicine, drug development and other fields.

WP4 aims to develop standardised format(s) for selected biophysical methods, tools for data curation, and a pilot database. In order to realize these tasks, mapping of the needs of the community in this area is a prerequisite. Mapping performed in the form of an electronic survey must take into account the variety of levels of knowledge, use, expectations, experience with databases and data management, and scientific backgrounds of the respondents.

The survey

An online survey was prepared in early 2022 and initially presented to the MOSBRI partners only, to allow refinement of the survey, before being opened publicly in February 2022. The survey consisted of 23 questions (see below) and primarily focused on the 30 biophysical techniques offered through MOSBRI. The survey was closed in mid-March 2022 having received 178 responses in total across the two rounds (MOSBRI and global).

The results show that there is a strong variation in the use and knowledge of the individual experimental techniques and of experience of data sharing, a generally low level of research data management at the respondents’ institutions, but also a recognized need for data sharing, format standardisation and repositories for many of the techniques listed. A significant number of respondents indicated their interest in collaborating in data standardisation. The results indicate the direction of future WP4 activities, highlighting needs for data standards and database development for specific biophysical methods used for protein characterisation and the study of biomolecular interactions.

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Results of the survey

Presented below are a selection of the results obtained in the survey, while all results can be viewed in the documents linked at the bottom of the page.

• Questions in the survey
• How many people completed the survey and who were they?
• Experience with data deposition
• What techniques are used and how much?
• Where are the highest needs for data standardisation?
• Conclusions from the survey
• Final deliverable report and annex 1 documents and raw data

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Questions in the survey

The survey questions were focused on identifying the expertise and scientific interests of the respondents, their use of techniques of molecular biophysics, views on the current situation and need for data format standardisation and needs for repositories or databases.

To view the full list of questions select “Questions asked in the survey” below:

Questions asked in the survey

 

How many people completed the survey and who were they?

The survey respondents were mostly from universities and public research organizations (93%), while 6% were from industry. 64% of respondents belonged to the categories principal investigator, senior researcher, or head of department and higher, while the student and post‐doc categories represented 18% of respondents (Figure Qu. 2). Respondents were mostly active in the general fields of biophysics, biochemistry, and molecular biology, with the other fields represented by significantly smaller numbers (Figure Qu. 3). Responses to question 4 about narrower research areas showed that most of the respondents were mainly active in molecular biophysics, structural biology, and recombinant protein production.

The survey respondents mostly study proteins, protein‐protein interactions, and protein‐nucleic acid interactions, while the other types of biomolecules were significantly less represented.

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Experience with data deposition

61% of respondents have had experience with data deposition into public databases or repositories, the PDB, SASBDB, and EMDB being mentioned most frequently. 49% of respondents have had experience with deposition of molecular biophysics and structural biology data (Question 8) and only 37% of respondents’ institutions supported systematic long-term storage of scientific data.

Figure Qu. 6: Have you ever deposited any scientific data into a public database/repository?

Several related efforts regarding management of biophysical data were mentioned by the respondents, mainly PCDDB, single crystal diffraction image repositories, CryoEM‐related efforts, MolMeDB, NMRlipids, an unspecified protein‐ligand binding database, and PDBDev (see Annex 1 for details).

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What techniques are used and how much?

The techniques being used by the highest number of respondents are CD, UV/VIS spectroscopy, fluorescence spectroscopy, DLS, ITC, and SPR (Figure Qu. 14).
The techniques more heavily used (i.e., frequency of usage) are UV/VIS spectroscopy, CD, fluorescence spectroscopy, DLS, ITC, fluorescence microscopy, DSF, and SPR (Figure Qu. 14).

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Where are the highest needs for data standardisation?

82% of all respondents see a high or relatively high need for data standardisation in molecular biophysics and a similar proportion perceive a high need for applying the FAIR principles in this field. Almost 90% of respondents acknowledge receiving benefit from access to scientific data made available according to FAIR principles.

The highest perceived need for sharing data with the whole scientific community (Question 15, see Annex 1) was identified for SAXS (72% of respondents), ssNMR 1D (59.6%), super‐resolution microscopy (57.6%), time‐resolved single particle fluorescence (55.4%), and then other techniques.

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Conclusions from the survey

The results of the survey on the needs for biophysical data standardisation and databases have shown the following points are important for the development of data standards, software tools, and a pilot database under WP4 of MOSBRI:

1. The community of users of the techniques of molecular biophysics is well aware of the needs of FAIR data management in this field and indicated a high level of need for data format standardisation and repositories for a number of techniques.
2. The relative use and number of users differ significantly across the individual techniques and this must be taken into account when focusing resources on particular techniques during the further activities of WP4.
3. The following techniques (among those included in the survey) show frequent use or high numbers of users.
   The top 10, shown in order from the highest, are: UV/VIS spectroscopy, CD, fluorescence spectroscopy, ITC, DLS/MADLS, fluorescence microscopy, SPR, DSF, MST, and DSC.
4. The following techniques (among those included in the survey) show a high need for data standards and for a repository
   The top 10, shown in order from the highest mean of normalized needs for standards and databases, are: MST, CD, SPR, DSC, SAXS, ssNMR 1D, BLI, mass photometry, (SEC)‐MALS, and ITC.
5. The results of the survey have identified other important projects related to WP4 of MOSBRI and opened up a number of new contacts for potential collaboration.
6. The survey results are of high value and will be fully exploited in further tasks under WP4.

 

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Final deliverable report, annex 1 documents and raw data

The final report describing the work carried out and the summary of results of the survey, as well as the supporting Annex 1 document containing full analysis of the responses to the questions, can be downloaded below by clicking the filenames under the images.

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List of abbreviations