CITATION.cff

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cff-version: 1.2.0
title: mite_extras
message: >-
  If you use this software, please cite the referenced
  paper.
type: software
authors:
  - affiliation: 'Wageningen University and Research'
    family-names: Zdouc
    given-names: Mitja M.
    orcid: 'https://orcid.org/0000-0001-6534-6609'
  - affiliation: 'Institute of Molecular Systems Biology, ETH Zürich'
    family-names: Rutz
    given-names: Adriano
    orcid: 'https://orcid.org/0000-0003-0443-9902'
repository-code: 'https://github.com/mite-standard/mite_extras'
abstract: >-
    Validation and conversion functionality for reaction SMARTS collected in the scope of MITE.
keywords:
  - python
  - tailoring enzymes
  - SMARTS
license: MIT
preferred-citation:
  type: article
  authors:
    - address: 'Otto-Stern-Weg 3, 8093 Zürich, Switzerland'
      affiliation: 'Institute for Molecular Systems Biology, ETH Zürich'
      family-names: Rutz
      given-names: Adriano
      orcid: 'https://orcid.org/0000-0003-0443-9902'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Bioinformatics Group, Wageningen University & Research'
      family-names: Probst
      given-names: Daniel
      orcid: 'https://orcid.org/0000-0003-1737-4407'
    - address: 'Av. Eugenio Garza Sada 2501 sur, Nuevo Leon, 64700, México'
      affiliation: 'Industrial Genomics Laboratory, Centro de Biotecnología FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey'
      family-names: Aguilar
      given-names: César
      orcid: 'https://orcid.org/0000-0001-7044-2419'
    - address: 'Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP)'
      affiliation: 'Rua Monteiro Lobato 270, Campinas, São Paulo, 13.083-862, Brazil'
      family-names: Akiyama
      given-names: Daniel Y.
      orcid: 'https://orcid.org/0000-0003-2859-1992'
    - address: 'Gibbet Hill Road, Coventry, CV4 7AL, UK'
      affiliation: 'School of Life Sciences, University of Warwick'
      family-names: Alberti
      given-names: Fabrizio
      orcid: 'https://orcid.org/0000-0001-6585-0696'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Bioinformatics Group, Wageningen University & Research'
      family-names: Augustijn
      given-names: Hannah E.
      orcid: 'https://orcid.org/0000-0002-1862-6699'
    - address: 'Irvine, 856 Health Sciences Road, Irvine, California, USA 92697'
      affiliation: 'Department of Pharmaceutical Sciences, University of California'
      family-names: Avalon
      given-names: Nicole E.
      orcid: 'https://orcid.org/0000-0003-3588-892X'
    - address: 'Campus E8.1, 66123 Saarbrücken, Germany'
      affiliation: 'Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI)'
      family-names: Beemelmanns
      given-names: Christine
      orcid: 'https://orcid.org/0000-0002-9747-3423'
    - address: 'Rua Monteiro Lobato 270, Campinas, São Paulo, 13.083-862, Brazil'
      affiliation: 'Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP)'
      family-names: Bertoletti Barbieri
      given-names: Hellen
      orcid: 'https://orcid.org/0000-0002-6270-3874'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Bioinformatics Group, Wageningen University & Research'
      family-names: Biermann
      given-names: Friederike
      orcid: 'https://orcid.org/0000-0002-9152-2562'
    - address: 'SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland'
      affiliation: 'SIB Swiss Institute of Bioinformatics'
      family-names: Bridge
      given-names: Alan J.
      orcid: 'https://orcid.org/0000-0003-2148-9135'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Bioinformatics Group, Wageningen University & Research'
      family-names: Charria Girón
      given-names: Esteban
      orcid: 'https://orcid.org/0000-0002-3823-1416'
    - address: 'Schneiderberg 38, 30167 Hannover, Germany'
      affiliation: 'Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover'
      family-names: Cox
      given-names: Russell
      orcid: 'https://orcid.org/0000-0002-1844-0157'
    - address: 'Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany'
      affiliation: 'Institute for Pharmaceutical Biology, Goethe University Frankfurt'
      family-names: Crüsemann
      given-names: Max
      orcid: 'https://orcid.org/0000-0001-6660-2715'
    - address: 'Campus E8.1, 66123 Saarbrücken, Germany'
      affiliation: 'Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI)'
      family-names: D'Agostino
      given-names: Paul M.
      orcid: 'https://orcid.org/0000-0002-8323-5416'
    - address: 'SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland'
      affiliation: 'SIB Swiss Institute of Bioinformatics'
      family-names: Feuermann
      given-names: Marc
      orcid: 'https://orcid.org/0000-0002-4187-2863'
    - address: 'Schneiderberg 38, 30167 Hannover, Germany'
      affiliation: 'Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover'
      family-names: Gerke
      given-names: Jennifer
      orcid: 'https://orcid.org/0000-0001-7301-2676'
    - address: '3520 San Martin Dr, Baltimore, MD, 21218, USA'
      affiliation: 'Biosphere Sciences and Engineering Division, Carnegie Institution for Science'
      family-names: Gutiérrez García
      given-names: Karina
      orcid: 'https://orcid.org/0000-0002-6077-7490'
    - address: 'P.O.Box 4760 Torgard, N-7465 Trondheim, Norway'
      affiliation: 'Department of Biotechnology and Nanomedicine, SINTEF Industry'
      family-names: Holme
      given-names: Jonathan E.
      orcid: 'https://orcid.org/0009-0007-1652-9477'
    - address: 'Frederick, Maryland 21702-1201, USA'
      affiliation: 'Molecular Targets Program, Center for Cancer Research, National Cancer Institute'
      family-names: Hwang
      given-names: Ji-Yeon
      orcid: 'https://orcid.org/0009-0005-0157-5724'
    - address: 'Maarintie 3, 02150 Espoo, Finland'
      affiliation: 'Production Host Engineering Team, VTT Technical Research Centre of Finland Ltd'
      family-names: Iacovelli
      given-names: Riccardo
      orcid: 'https://orcid.org/0000-0003-4819-2251'
    - address: 'Rua Monteiro Lobato 270, Campinas, São Paulo, 13.083-862, Brazil'
      affiliation: 'Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP)'
      family-names: Jeronimo Barbosa
      given-names: Júlio César
      orcid: 'https://orcid.org/0000-0001-8831-831X'
    - address: 'Sector 81, S.A.S. Nagar, Mohali, Punjab 140306, India'
      affiliation: 'Computational Biology Lab, National Agri-Food and Biomanufacturing Institute (NABI)'
      family-names: Kaur
      given-names: Navneet
      orcid: 'https://orcid.org/0009-0002-2037-5945'
    - address: 'Beutenbergstr. 11a, 07745 Jena, Germany'
      affiliation: 'Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute'
      family-names: Klapper
      given-names: Martin
      orcid: 'https://orcid.org/0000-0002-4977-2541'
    - address: 'Schneiderberg 38, 30167 Hannover, Germany'
      affiliation: 'Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover'
      family-names: Köhler
      given-names: Anna M.
      orcid: 'https://orcid.org/0000-0002-2715-8954'
    - address: 'Auf der Morgenstelle 24, 72076 Tübingen, Germany'
      affiliation: 'Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen'
      family-names: Korenskaia
      given-names: Aleksandra
      orcid: 'https://orcid.org/0000-0003-3002-6458'
    - address: 'Auf der Morgenstelle 24, 72076 Tübingen, Germany'
      affiliation: 'Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen'
      family-names: Kubach
      given-names: Noel
      orcid: 'https://orcid.org/0009-0008-7609-4484'
    - address: 'Daejeon 34141, Republic of Korea'
      affiliation: 'Institute of Applied Sciences, Korea Advanced Institute of Science and Technology (KAIST)'
      family-names: Lee
      given-names: Byung T.
      orcid: 'https://orcid.org/0009-0008-3623-3734'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Bioinformatics Group, Wageningen University & Research'
      family-names: Loureiro
      given-names: Catarina
      orcid: 'https://orcid.org/0000-0002-6258-2080'
    - address: 'Sector 81, S.A.S. Nagar, Mohali, Punjab 140306, India'
      affiliation: 'Computational Biology Lab, National Agri-Food and Biomanufacturing Institute (NABI)'
      family-names: Mantri
      given-names: Shrikant
      orcid: 'https://orcid.org/0000-0002-7493-459X'
    - address: 'Sector 81, S.A.S. Nagar, Mohali, Punjab 140306, India'
      affiliation: 'Computational Biology Lab, National Agri-Food and Biomanufacturing Institute (NABI)'
      family-names: Narula
      given-names: Simran
      orcid: 'https://orcid.org/0009-0001-9399-9671'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Bioinformatics Group, Wageningen University & Research'
      family-names: Meijer
      given-names: David
      orcid: 'https://orcid.org/0000-0001-6406-4394'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Bioinformatics Group, Wageningen University & Research'
      family-names: Navarro-Muñoz
      given-names: Jorge C.
      orcid: 'https://orcid.org/0000-0003-2992-1607'
    - address: 'P.O.Box 4760 Torgard, N-7465 Trondheim, Norway'
      affiliation: 'Department of Biotechnology and Nanomedicine, SINTEF Industry'
      family-names: Nguyen
      given-names: Giang-Son
      orcid: 'https://orcid.org/0000-0001-5730-3326'
    - address: 'Sector 81, S.A.S. Nagar, Mohali, Punjab 140306, India'
      affiliation: 'Computational Biology Lab, National Agri-Food and Biomanufacturing Institute (NABI)'
      family-names: Paliyal
      given-names: Sunaina
      orcid: 'https://orcid.org/0009-0003-1714-1678'
    - address: 'Sector 81, S.A.S. Nagar, Mohali, Punjab 140306, India'
      affiliation: 'Computational Biology Lab, National Agri-Food and Biomanufacturing Institute (NABI)'
      family-names: Panghal
      given-names: Mohit
      orcid: 'https://orcid.org/0009-0001-3436-5302'
    - address: 'Sector 81, S.A.S. Nagar, Mohali, Punjab 140306, India'
      affiliation: 'Computational Biology Lab, National Agri-Food and Biomanufacturing Institute (NABI)'
      family-names: Latika
      given-names: Latika
      orcid: 'https://orcid.org/0009-0000-2169-0598'
    - address: 'Winterthurerstrasse 190, 8057 Zurich, Switzerland'
      affiliation: 'Department of Chemistry, University of Zurich'
      family-names: Sieber
      given-names: Simon
      orcid: 'https://orcid.org/0000-0003-1763-2525'
    - address: 'Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands'
      affiliation: 'Department of Chemical and Pharmaceutical Biology, University of Groningen'
      family-names: Sokolova
      given-names: Nika
      orcid: 'https://orcid.org/0000-0003-4129-2890'
    - address: 'Klingelbergstrasse 50, 4056 Basel, Switzerland'
      affiliation: 'Department of Pharmaceutical Sciences, University of Basel'
      family-names: Sowa
      given-names: Sven T.
      orcid: 'https://orcid.org/0000-0001-7411-5925'
    - address: 'Building 220, Søltofts Plads, 2800 Kongens Lyngby, Denmark'
      affiliation: 'The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark'
      family-names: Szenei
      given-names: Judit
      orcid: 'https://orcid.org/0009-0006-9871-5187'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Bioinformatics Group, Wageningen University & Research'
      family-names: Terlouw
      given-names: Barbara R.
      orcid: 'https://orcid.org/0000-0002-4058-6718'
    - address: 'Klingelbergstrasse 50, 4056 Basel, Switzerland'
      affiliation: 'Department of Pharmaceutical Sciences, University of Basel'
      family-names: Weddeling
      given-names: Heiner G.
      orcid: 'https://orcid.org/0009-0003-2819-1486'
    - address: '1088 Xueyuan Avenue, Shenzhen 518055, P.R. China'
      affiliation: 'Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology'
      family-names: Yu
      given-names: Jingwei
      orcid: 'https://orcid.org/0000-0003-4268-436X'
    - address: 'Auf der Morgenstelle 24, 72076 Tübingen, Germany'
      affiliation: 'Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen'
      family-names: Ziemert
      given-names: Nadine
      orcid: 'https://orcid.org/0000-0002-7264-1857'
    - address: 'Building 220, Søltofts Plads, 2800 Kongens Lyngby, Denmark'
      affiliation: 'The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark'
      family-names: Weber
      given-names: Tilmann
      orcid: 'https://orcid.org/0000-0002-8260-5120'
    - address: 'Building 220, Søltofts Plads, 2800 Kongens Lyngby, Denmark'
      affiliation: 'The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark'
      family-names: Blin
      given-names: Kai
      orcid: 'https://orcid.org/0000-0003-3764-6051'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Bioinformatics Group, Wageningen University & Research'
      family-names: van der Hooft
      given-names: Justin J.J.
      orcid: 'https://orcid.org/0000-0002-9340-5511'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Bioinformatics Group, Wageningen University & Research'
      family-names: Medema
      given-names: Marnix H.
      orcid: 'https://orcid.org/0000-0002-2191-2821'
    - address: 'Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands'
      affiliation: 'Bioinformatics Group, Wageningen University & Research'
      family-names: Zdouc
      given-names: Mitja M.
      orcid: 'https://orcid.org/0000-0001-6534-6609'
  title: 'MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis'
  journal: Nucleic Acids Research
  year: 2025
  doi: 10.1093/nar/gkaf969