Multi Locus Sequence Typing Policy Document (Tenacibaculum)

  1. The primary purpose of the Multi Locus Sequence Typing (hereafter MLST) website is for the typing and global epidemiology of bacterial pathogens. Data analysis for research should be viewed as a secondary objective.
  2. The Tenacibaculum MLST website is located and managed at the Department of Zoology, University of Oxford, which provides the resources for this project. The persons responsible for the site (hereafter the Management Team) are as follows:
    • Database curator: Christophe Habib
    • Website Manager: Keith Jolley (hereafter, the webmaster)

    Apart from verifying and managing all data submitted to the databases, the above persons will not have any special privileges with regard to the analysis or publication of data compared to other users.

  3. Although the web site is located in Oxford, we see the project as a joint project of the scientific community in this field and welcome all users to submit their MLST data in order to strengthen the resource. For reasons of security and accountability, we require that all submitters of data are registered with the curator and provide an email address or other means of communication.
  4. There are two main databases accessible from the Tenacibaculum website and the policy for submissions are as follows:

    Profiles database

    All assignments of new sequence types and new alleles will be done by the curator and/or the webmaster and responsibility for the consistency and uniqueness of these rests with the Management Team.

    • For the submission of new allelic profiles consisting of existing alleles, the user is requested to send the data to the curator with the alleles already assigned (rather than sending sequence trace files). Therefore the responsibility of correct allele assignment rests with the user.  For each sequence type in the profiles database, we require an example isolate to be submitted to the PubMLST isolate database.
    • All requests for new allele numbers should be accompanied by forward and reverse trace files sent to the relevant curator who will be responsible for correct assignment of alleles.

    PubMLST isolate database

    • Since the timely identification of new strains is important for epidemiological purposes, we encourage the early submission of data to the web site. Therefore some of the data will be unpublished. The Management Team will make all reasonable efforts to protect unpublished data on behalf of the submitters according to the guidelines in the points below. For the purposes of this document we define published data as those which have been published in a journal or book OR are available on Genbank. Unpublished data belong to the original submitters. However, the Management Team cannot be held responsible for the misuse of data.
  5. The objective is that the website will contain basic and advanced facilities for querying the databases and data analysis tools for drawing trees, graphs and maps etc and statistical analysis. The results of these queries and analyses may be used and published by the users on the condition that permission is obtained to use unpublished data. However, the website and the Wellcome Trust must be acknowledged in all publications. The user may also save copies of the subset of the databases obtained as a result of these queries on their local computer but may not publish it on a web server without prior consent of the webmaster. Data submitters should be aware that their data may be used in this way.
  6. The preferred format of the acknowledgement is: This publication made use of the Tenacibaculum Multi Locus Sequence Typing website (http://pubmlst.org/tenacibaculum/) developed by Keith Jolley (Jolley & Maiden 2010, BMC Bioinformatics, 11:595) and sited at the University of Oxford. The development of this site has been funded by the Wellcome Trust.
  7. In order to encourage maximum participation in submission of data and to prevent the proliferation of copies of the databases, it is not our policy to provide a direct download of the whole isolate database from the website.
  8. Although it is not the main purpose of the website, we appreciate that the isolate database may provide additional opportunities for data analysis for research purposes, which we do not intend to provide directly on the site. Individual users wishing to do such analyses may apply to the webmaster for a copy of the database with an explanation of the type of analysis to be done. Normally, this would involve a subset of the database and would be a copy valid for a particular date. Users wishing to use this service are subject to the following conditions (9 and 10).  
  9. Users of special copies of the database should obtain permission from owners of any unpublished data in their copy for publication purposes. The webmaster will provide a list of these data owners for this purpose.
  10. In order to avoid a situation where there are many copies of the databases in the public domain, users with copies of the databases may not produce their own database driven web server and may not distribute the databases to third parties. In any case, the databases on the MLST site will be deemed the Master copies.
  11. As stated in (2), the Management Team will not have special privileges to analyse unpublished data for research purposes without the prior consent of the data owners. However, we do reserve the right to provide 'current status' information on the website or in review articles including broad breakdowns by serogroup, country etc.
  12. A full copy of the profiles database is extracted as a text file each night and is available for download from the website.  Allele sequence files are available in the same way.
  13. We reserve the right to enforce stronger security if we detect abuse of the website.

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Citing the database

The preferred format for citing this website in publications is:

This publication made use of the Tenacibaculum MLST website (https://pubmlst.org/ tenacibaculum/) sited at the University of Oxford (Jolley et al. Wellcome Open Res 2018, 3:124 [version 1; referees: 2 approved]). The development of this site has been funded by the Wellcome Trust.

Status

Sequence database
Sequences: 407
Profiles (MLST): 125
Last updated: 2016-12-23

Isolate database
Isolates: 114
Last updated: 2016-08-04