DisProt: Intrinsic protein disorder annotation in 2020

András Hatos; Borbála Hajdu-Soltész; Alexander M. Monzon; Nicolas Palopoli; Lucía Álvarez; Burcu Aykac-Fas; Claudio Bassot; Guillermo I. Benítez; Martina Bevilacqua; Anastasia Chasapi; Lucia Chemes; Norman E. Davey; Radoslav Davidović; A. Keith Dunker; Arne Elofsson; Julien Gobeill; Nicolás S.González Foutel; Govindarajan Sudha; Mainak Guharoy; Tamas Horvath; Valentin Iglesias; Andrey V. Kajava; Orsolya P. Kovacs; John Lamb; Matteo Lambrughi; Tamas Lazar; Jeremy Y. Leclercq; Emanuela Leonardi; Sandra MacEdo-Ribeiro; Mauricio MacOssay-Castillo; Emiliano Maiani; José A. Manso; Cristina Marino-Buslje; Elizabeth Martínez-Pérez; Bálint Mészáros; Ivan Mičetić; Giovanni Minervini; Nikoletta Murvai; Marco Necci; Christos A. Ouzounis; Mátyás Pajkos; Lisanna Paladin; Rita Pancsa; Elena Papaleo; Gustavo Parisi; Emilie Pasche; Pedro J. Barbosa Pereira; Vasilis J. Promponas; Jordi Pujols; Federica Quaglia; Patrick Ruch; Marco Salvatore; Eva Schad; Beata Szabo; Tamás Szaniszló; Stella Tamana; Agnes Tantos; Nevena Veljkovic; Salvador Ventura; Wim Vranken; Zsuzsanna Dosztányi; Peter Tompa; Silvio C.E. Tosatto; Damiano Piovesan

doi:10.1093/nar/gkz975

DisProt: Intrinsic protein disorder annotation in 2020

András Hatos, Borbála Hajdu-Soltész, Alexander M. Monzon, Nicolas Palopoli, Lucía Álvarez, Burcu Aykac-Fas, Claudio Bassot, Guillermo I. Benítez, Martina Bevilacqua, Anastasia Chasapi, Lucia Chemes, Norman E. Davey, Radoslav Davidović, A. Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S.González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamas HorvathValentin Iglesias, Andrey V. Kajava, Orsolya P. Kovacs, John Lamb, Matteo Lambrughi, Tamas Lazar, Jeremy Y. Leclercq, Emanuela Leonardi, Sandra MacEdo-Ribeiro, Mauricio MacOssay-Castillo, Emiliano Maiani, José A. Manso, Cristina Marino-Buslje, Elizabeth Martínez-Pérez, Bálint Mészáros, Ivan Mičetić, Giovanni Minervini, Nikoletta Murvai, Marco Necci, Christos A. Ouzounis, Mátyás Pajkos, Lisanna Paladin, Rita Pancsa, Elena Papaleo, Gustavo Parisi, Emilie Pasche, Pedro J. Barbosa Pereira, Vasilis J. Promponas, Jordi Pujols, Federica Quaglia, Patrick Ruch, Marco Salvatore, Eva Schad, Beata Szabo, Tamás Szaniszló, Stella Tamana, Agnes Tantos, Nevena Veljkovic, Salvador Ventura, Wim Vranken, Zsuzsanna Dosztányi, Peter Tompa, Silvio C.E. Tosatto^*, Damiano Piovesan

^*Corresponding author af dette arbejde

Brunak Group

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

195 Citationer (Scopus)

19 Downloads (Pure)

Abstract

The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome.

Originalsprog	Engelsk
Tidsskrift	Nucleic Acids Research
Vol/bind	48
Udgave nummer	D1
Sider (fra-til)	D269-D276
ISSN	0305-1048
DOI	https://doi.org/10.1093/nar/gkz975
Status	Udgivet - 2020

Bibliografisk note

Funding Information:
Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) of Argentina [PICT-2015/3367, PICT-2017/1924]; Ministry of Education, Science and Technological Development of the Republic of Serbia [ON173001]; Vetenskapsrådet [2016-03798]; Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133]; Italian Ministry of Health Young Investigator Grant [GR-2011-02347754]; Ministerio de Economía y Competitividad (MINECO) [BIO2016-78310-R]; ICREA (ICREA-Academia 2015); Fundac¸ão para a Ciência e a Tecnologia (FCT, Portugal); European Regional Development Fund [POCI-01-0145-FEDER-031173, POCI-01-0145-FEDER-029221]; Mexican National Council of Science and Technology (CONACYT) [215503]; Elixir-GR, Action ‘Reinforcement of the Research and Innovation Infrastructure’, Operational Programme ‘Competitiveness, Entrepreneurship and Innovation’ [NSRF 2014-2020]. co-financed by Greece and the European Union (European Regional Development Fund); Hungarian Academy of Sciences [PREMIUM-2017-48]; Carlsberg Distinguished Fellowship [CF18-0314]; Danmarks Grundforskningsfond [DNRF125]; National Research, Development and Innovation Office [K-125340]; Research Foundation Flanders (FWO) [G.0328.16N]; Hungarian Academy of Sciences [LP2014-18]; OTKA [K108798 and K124670]. This project has received funding from the European Union’s Horizon 2020 research and innovation programme [778247]. Funding for open access charge: European Union’s Horizon 2020 research and innovation programme [778247]. Conflict of interest statement. None declared.

Publisher Copyright:
© 2019 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.

Adgang til dokumentet

10.1093/nar/gkz975Licens: CC BY

DisProt: intrinsic protein disorder annotation in 2020Forlagets udgivne version, 679 KBLicens: CC BY

Citationsformater

Hatos, A., Hajdu-Soltész, B., Monzon, A. M., Palopoli, N., Álvarez, L., Aykac-Fas, B., Bassot, C., Benítez, G. I., Bevilacqua, M., Chasapi, A., Chemes, L., Davey, N. E., Davidović, R., Dunker, A. K., Elofsson, A., Gobeill, J., Foutel, N. S. G., Sudha, G., Guharoy, M., ... Piovesan, D. (2020). DisProt: Intrinsic protein disorder annotation in 2020. Nucleic Acids Research, 48(D1), D269-D276. https://doi.org/10.1093/nar/gkz975

DisProt : Intrinsic protein disorder annotation in 2020. / Hatos, András; Hajdu-Soltész, Borbála; Monzon, Alexander M.; Palopoli, Nicolas; Álvarez, Lucía; Aykac-Fas, Burcu; Bassot, Claudio; Benítez, Guillermo I.; Bevilacqua, Martina; Chasapi, Anastasia; Chemes, Lucia; Davey, Norman E.; Davidović, Radoslav; Dunker, A. Keith; Elofsson, Arne; Gobeill, Julien; Foutel, Nicolás S.González; Sudha, Govindarajan; Guharoy, Mainak; Horvath, Tamas; Iglesias, Valentin; Kajava, Andrey V.; Kovacs, Orsolya P.; Lamb, John; Lambrughi, Matteo; Lazar, Tamas; Leclercq, Jeremy Y.; Leonardi, Emanuela; MacEdo-Ribeiro, Sandra; MacOssay-Castillo, Mauricio; Maiani, Emiliano; Manso, José A.; Marino-Buslje, Cristina; Martínez-Pérez, Elizabeth; Mészáros, Bálint; Mičetić, Ivan; Minervini, Giovanni; Murvai, Nikoletta; Necci, Marco; Ouzounis, Christos A.; Pajkos, Mátyás; Paladin, Lisanna; Pancsa, Rita; Papaleo, Elena; Parisi, Gustavo; Pasche, Emilie; Barbosa Pereira, Pedro J.; Promponas, Vasilis J.; Pujols, Jordi; Quaglia, Federica; Ruch, Patrick; Salvatore, Marco; Schad, Eva; Szabo, Beata; Szaniszló, Tamás; Tamana, Stella; Tantos, Agnes; Veljkovic, Nevena; Ventura, Salvador; Vranken, Wim; Dosztányi, Zsuzsanna; Tompa, Peter; Tosatto, Silvio C.E.; Piovesan, Damiano.

I: Nucleic Acids Research, Bind 48, Nr. D1, 2020, s. D269-D276.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

Hatos, A, Hajdu-Soltész, B, Monzon, AM, Palopoli, N, Álvarez, L, Aykac-Fas, B, Bassot, C, Benítez, GI, Bevilacqua, M, Chasapi, A, Chemes, L, Davey, NE, Davidović, R, Dunker, AK, Elofsson, A, Gobeill, J, Foutel, NSG, Sudha, G, Guharoy, M, Horvath, T, Iglesias, V, Kajava, AV, Kovacs, OP, Lamb, J, Lambrughi, M, Lazar, T, Leclercq, JY, Leonardi, E, MacEdo-Ribeiro, S, MacOssay-Castillo, M, Maiani, E, Manso, JA, Marino-Buslje, C, Martínez-Pérez, E, Mészáros, B, Mičetić, I, Minervini, G, Murvai, N, Necci, M, Ouzounis, CA, Pajkos, M, Paladin, L, Pancsa, R, Papaleo, E, Parisi, G, Pasche, E, Barbosa Pereira, PJ, Promponas, VJ, Pujols, J, Quaglia, F, Ruch, P, Salvatore, M, Schad, E, Szabo, B, Szaniszló, T, Tamana, S, Tantos, A, Veljkovic, N, Ventura, S, Vranken, W, Dosztányi, Z, Tompa, P, Tosatto, SCE & Piovesan, D 2020, 'DisProt: Intrinsic protein disorder annotation in 2020', Nucleic Acids Research, bind 48, nr. D1, s. D269-D276. https://doi.org/10.1093/nar/gkz975

Hatos, András ; Hajdu-Soltész, Borbála ; Monzon, Alexander M. ; Palopoli, Nicolas ; Álvarez, Lucía ; Aykac-Fas, Burcu ; Bassot, Claudio ; Benítez, Guillermo I. ; Bevilacqua, Martina ; Chasapi, Anastasia ; Chemes, Lucia ; Davey, Norman E. ; Davidović, Radoslav ; Dunker, A. Keith ; Elofsson, Arne ; Gobeill, Julien ; Foutel, Nicolás S.González ; Sudha, Govindarajan ; Guharoy, Mainak ; Horvath, Tamas ; Iglesias, Valentin ; Kajava, Andrey V. ; Kovacs, Orsolya P. ; Lamb, John ; Lambrughi, Matteo ; Lazar, Tamas ; Leclercq, Jeremy Y. ; Leonardi, Emanuela ; MacEdo-Ribeiro, Sandra ; MacOssay-Castillo, Mauricio ; Maiani, Emiliano ; Manso, José A. ; Marino-Buslje, Cristina ; Martínez-Pérez, Elizabeth ; Mészáros, Bálint ; Mičetić, Ivan ; Minervini, Giovanni ; Murvai, Nikoletta ; Necci, Marco ; Ouzounis, Christos A. ; Pajkos, Mátyás ; Paladin, Lisanna ; Pancsa, Rita ; Papaleo, Elena ; Parisi, Gustavo ; Pasche, Emilie ; Barbosa Pereira, Pedro J. ; Promponas, Vasilis J. ; Pujols, Jordi ; Quaglia, Federica ; Ruch, Patrick ; Salvatore, Marco ; Schad, Eva ; Szabo, Beata ; Szaniszló, Tamás ; Tamana, Stella ; Tantos, Agnes ; Veljkovic, Nevena ; Ventura, Salvador ; Vranken, Wim ; Dosztányi, Zsuzsanna ; Tompa, Peter ; Tosatto, Silvio C.E. ; Piovesan, Damiano. / DisProt : Intrinsic protein disorder annotation in 2020. I: Nucleic Acids Research. 2020 ; Bind 48, Nr. D1. s. D269-D276.

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title = "DisProt: Intrinsic protein disorder annotation in 2020",

abstract = "The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome.",

author = "Andr{\'a}s Hatos and Borb{\'a}la Hajdu-Solt{\'e}sz and Monzon, {Alexander M.} and Nicolas Palopoli and Luc{\'i}a {\'A}lvarez and Burcu Aykac-Fas and Claudio Bassot and Ben{\'i}tez, {Guillermo I.} and Martina Bevilacqua and Anastasia Chasapi and Lucia Chemes and Davey, {Norman E.} and Radoslav Davidovi{\'c} and Dunker, {A. Keith} and Arne Elofsson and Julien Gobeill and Foutel, {Nicol{\'a}s S.Gonz{\'a}lez} and Govindarajan Sudha and Mainak Guharoy and Tamas Horvath and Valentin Iglesias and Kajava, {Andrey V.} and Kovacs, {Orsolya P.} and John Lamb and Matteo Lambrughi and Tamas Lazar and Leclercq, {Jeremy Y.} and Emanuela Leonardi and Sandra MacEdo-Ribeiro and Mauricio MacOssay-Castillo and Emiliano Maiani and Manso, {Jos{\'e} A.} and Cristina Marino-Buslje and Elizabeth Mart{\'i}nez-P{\'e}rez and B{\'a}lint M{\'e}sz{\'a}ros and Ivan Mi{\v c}eti{\'c} and Giovanni Minervini and Nikoletta Murvai and Marco Necci and Ouzounis, {Christos A.} and M{\'a}ty{\'a}s Pajkos and Lisanna Paladin and Rita Pancsa and Elena Papaleo and Gustavo Parisi and Emilie Pasche and {Barbosa Pereira}, {Pedro J.} and Promponas, {Vasilis J.} and Jordi Pujols and Federica Quaglia and Patrick Ruch and Marco Salvatore and Eva Schad and Beata Szabo and Tam{\'a}s Szaniszl{\'o} and Stella Tamana and Agnes Tantos and Nevena Veljkovic and Salvador Ventura and Wim Vranken and Zsuzsanna Doszt{\'a}nyi and Peter Tompa and Tosatto, {Silvio C.E.} and Damiano Piovesan",

note = "Funding Information: Agencia Nacional de Promoci{\'o}n Cient{\'i}fica y Tecnol{\'o}gica (ANPCyT) of Argentina [PICT-2015/3367, PICT-2017/1924]; Ministry of Education, Science and Technological Development of the Republic of Serbia [ON173001]; Vetenskapsr{\aa}det [2016-03798]; Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133]; Italian Ministry of Health Young Investigator Grant [GR-2011-02347754]; Ministerio de Econom{\'i}a y Competitividad (MINECO) [BIO2016-78310-R]; ICREA (ICREA-Academia 2015); Fundac¸{\~a}o para a Ci{\^e}ncia e a Tecnologia (FCT, Portugal); European Regional Development Fund [POCI-01-0145-FEDER-031173, POCI-01-0145-FEDER-029221]; Mexican National Council of Science and Technology (CONACYT) [215503]; Elixir-GR, Action {\textquoteleft}Reinforcement of the Research and Innovation Infrastructure{\textquoteright}, Operational Programme {\textquoteleft}Competitiveness, Entrepreneurship and Innovation{\textquoteright} [NSRF 2014-2020]. co-financed by Greece and the European Union (European Regional Development Fund); Hungarian Academy of Sciences [PREMIUM-2017-48]; Carlsberg Distinguished Fellowship [CF18-0314]; Danmarks Grundforskningsfond [DNRF125]; National Research, Development and Innovation Office [K-125340]; Research Foundation Flanders (FWO) [G.0328.16N]; Hungarian Academy of Sciences [LP2014-18]; OTKA [K108798 and K124670]. This project has received funding from the European Union{\textquoteright}s Horizon 2020 research and innovation programme [778247]. Funding for open access charge: European Union{\textquoteright}s Horizon 2020 research and innovation programme [778247]. Conflict of interest statement. None declared. Publisher Copyright: {\textcopyright} 2019 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2020",

doi = "10.1093/nar/gkz975",

language = "English",

volume = "48",

pages = "D269--D276",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

TY - JOUR

T1 - DisProt

T2 - Intrinsic protein disorder annotation in 2020

AU - Hatos, András

AU - Hajdu-Soltész, Borbála

AU - Monzon, Alexander M.

AU - Palopoli, Nicolas

AU - Álvarez, Lucía

AU - Aykac-Fas, Burcu

AU - Bassot, Claudio

AU - Benítez, Guillermo I.

AU - Bevilacqua, Martina

AU - Chasapi, Anastasia

AU - Chemes, Lucia

AU - Davey, Norman E.

AU - Davidović, Radoslav

AU - Dunker, A. Keith

AU - Elofsson, Arne

AU - Gobeill, Julien

AU - Foutel, Nicolás S.González

AU - Sudha, Govindarajan

AU - Guharoy, Mainak

AU - Horvath, Tamas

AU - Iglesias, Valentin

AU - Kajava, Andrey V.

AU - Kovacs, Orsolya P.

AU - Lamb, John

AU - Lambrughi, Matteo

AU - Lazar, Tamas

AU - Leclercq, Jeremy Y.

AU - Leonardi, Emanuela

AU - MacEdo-Ribeiro, Sandra

AU - MacOssay-Castillo, Mauricio

AU - Maiani, Emiliano

AU - Manso, José A.

AU - Marino-Buslje, Cristina

AU - Martínez-Pérez, Elizabeth

AU - Mészáros, Bálint

AU - Mičetić, Ivan

AU - Minervini, Giovanni

AU - Murvai, Nikoletta

AU - Necci, Marco

AU - Ouzounis, Christos A.

AU - Pajkos, Mátyás

AU - Paladin, Lisanna

AU - Pancsa, Rita

AU - Papaleo, Elena

AU - Parisi, Gustavo

AU - Pasche, Emilie

AU - Barbosa Pereira, Pedro J.

AU - Promponas, Vasilis J.

AU - Pujols, Jordi

AU - Quaglia, Federica

AU - Ruch, Patrick

AU - Salvatore, Marco

AU - Schad, Eva

AU - Szabo, Beata

AU - Szaniszló, Tamás

AU - Tamana, Stella

AU - Tantos, Agnes

AU - Veljkovic, Nevena

AU - Ventura, Salvador

AU - Vranken, Wim

AU - Dosztányi, Zsuzsanna

AU - Tompa, Peter

AU - Tosatto, Silvio C.E.

AU - Piovesan, Damiano

N1 - Funding Information: Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) of Argentina [PICT-2015/3367, PICT-2017/1924]; Ministry of Education, Science and Technological Development of the Republic of Serbia [ON173001]; Vetenskapsrådet [2016-03798]; Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133]; Italian Ministry of Health Young Investigator Grant [GR-2011-02347754]; Ministerio de Economía y Competitividad (MINECO) [BIO2016-78310-R]; ICREA (ICREA-Academia 2015); Fundac¸ão para a Ciência e a Tecnologia (FCT, Portugal); European Regional Development Fund [POCI-01-0145-FEDER-031173, POCI-01-0145-FEDER-029221]; Mexican National Council of Science and Technology (CONACYT) [215503]; Elixir-GR, Action ‘Reinforcement of the Research and Innovation Infrastructure’, Operational Programme ‘Competitiveness, Entrepreneurship and Innovation’ [NSRF 2014-2020]. co-financed by Greece and the European Union (European Regional Development Fund); Hungarian Academy of Sciences [PREMIUM-2017-48]; Carlsberg Distinguished Fellowship [CF18-0314]; Danmarks Grundforskningsfond [DNRF125]; National Research, Development and Innovation Office [K-125340]; Research Foundation Flanders (FWO) [G.0328.16N]; Hungarian Academy of Sciences [LP2014-18]; OTKA [K108798 and K124670]. This project has received funding from the European Union’s Horizon 2020 research and innovation programme [778247]. Funding for open access charge: European Union’s Horizon 2020 research and innovation programme [778247]. Conflict of interest statement. None declared. Publisher Copyright: © 2019 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2020

Y1 - 2020

N2 - The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome.

AB - The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome.

U2 - 10.1093/nar/gkz975

DO - 10.1093/nar/gkz975

M3 - Journal article

C2 - 31713636

AN - SCOPUS:85077666918

VL - 48

SP - D269-D276

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - D1

ER -