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4. Correction for Vangay et al., “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities”

Author

Vangay, Pajau, Burgin, Josephine, Johnston, Anjanette, Beck, Kristen L, Berrios, Daniel C, Blumberg, Kai, Canon, Shane, Chain, Patrick, Chandonia, John-Marc, Christianson, Danielle, Costes, Sylvain V, Damerow, Joan, Duncan, William D, Dundore-Arias, Jose Pablo, Fagnan, Kjiersten, Galazka, Jonathan M, Gibbons, Sean M, Hays, David, Hervey, Judson, Hu, Bin, Hurwitz, Bonnie L, Jaiswal, Pankaj, Joachimiak, Marcin P, Kinkel, Linda, Ladau, Joshua, Martin, Stanton L, McCue, Lee Ann, Miller, Kayd, Mouncey, Nigel, Mungall, Chris, Pafilis, Evangelos, Reddy, TBK, Richardson, Lorna, Roux, Simon, Schriml, Lynn M, Shaffer, Justin P, Sundaramurthi, Jagadish Chandrabose, Thompson, Luke R, Timme, Ruth E, Zheng, Jie, Wood-Charlson, Elisha M, and Eloe-Fadrosh, Emiley A

Abstract

Volume 6, no. 1, e01194-20, 2021, https://doi.org/10.1128/mSystems.01194-20. The article byline and affiliation line should read as given in this correction.

Published
2021

5. Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

Author

Vangay, Pajau, Burgin, Josephine, Johnston, Anjanette, Beck, Kristen L, Berrios, Daniel C, Blumberg, Kai, Canon, Shane, Chain, Patrick, Chandonia, John-Marc, Christianson, Danielle, Costes, Sylvain V, Damerow, Joan, Duncan, William D, Dundore-Arias, Jose Pablo, Fagnan, Kjiersten, Galazka, Jonathan M, Gibbons, Sean M, Hays, David, Hervey, Judson, Hu, Bin, Hurwitz, Bonnie L, Jaiswal, Pankaj, Joachimiak, Marcin P, Kinkel, Linda, Ladau, Joshua, Martin, Stanton L, McCue, Lee Ann, Miller, Kayd, Mouncey, Nigel, Mungall, Chris, Pafilis, Evangelos, Reddy, TBK, Richardson, Lorna, Roux, Simon, Schriml, Lynn M, Shaffer, Justin P, Sundaramurthi, Jagadish Chandrabose, Thompson, Luke R, Timme, Ruth E, Zheng, Jie, Wood-Charlson, Elisha M, and Eloe-Fadrosh, Emiley A

Subjects
Information and Computing Sciences, Biological Sciences, Library and Information Studies, Microbiome, data standards, metadata, microbiome, ontology
Abstract

Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical. Important contributions have been made in the development of community-driven metadata standards; however, these standards have not been uniformly embraced by the microbiome research community. To understand how these standards are being adopted, or the barriers to adoption, across research domains, institutions, and funding agencies, the National Microbiome Data Collaborative (NMDC) hosted a workshop in October 2019. This report provides a summary of discussions that took place throughout the workshop, as well as outcomes of the working groups initiated at the workshop.

Published
2021

6. The Gene Ontology resource: enriching a GOld mine

Author

Carbon, Seth, Douglass, Eric, Good, Benjamin M, Unni, Deepak R, Harris, Nomi L, Mungall, Christopher J, Basu, Siddartha, Chisholm, Rex L, Dodson, Robert J, Hartline, Eric, Fey, Petra, Thomas, Paul D, Albou, Laurent-Philippe, Ebert, Dustin, Kesling, Michael J, Mi, Huaiyu, Muruganujan, Anushya, Huang, Xiaosong, Mushayahama, Tremayne, LaBonte, Sandra A, Siegele, Deborah A, Antonazzo, Giulia, Attrill, Helen, Brown, Nick H, Garapati, Phani, Marygold, Steven J, Trovisco, Vitor, dos Santos, Gil, Falls, Kathleen, Tabone, Christopher, Zhou, Pinglei, Goodman, Joshua L, Strelets, Victor B, Thurmond, Jim, Garmiri, Penelope, Ishtiaq, Rizwan, Rodríguez-López, Milagros, Acencio, Marcio L, Kuiper, Martin, Lægreid, Astrid, Logie, Colin, Lovering, Ruth C, Kramarz, Barbara, Saverimuttu, Shirin CC, Pinheiro, Sandra M, Gunn, Heather, Su, Renzhi, Thurlow, Katherine E, Chibucos, Marcus, Giglio, Michelle, Nadendla, Suvarna, Munro, James, Jackson, Rebecca, Duesbury, Margaret J, Del-Toro, Noemi, Meldal, Birgit HM, Paneerselvam, Kalpana, Perfetto, Livia, Porras, Pablo, Orchard, Sandra, Shrivastava, Anjali, Chang, Hsin-Yu, Finn, Robert Daniel, Mitchell, Alexander Lawson, Rawlings, Neil David, Richardson, Lorna, Sangrador-Vegas, Amaia, Blake, Judith A, Christie, Karen R, Dolan, Mary E, Drabkin, Harold J, Hill, David P, Ni, Li, Sitnikov, Dmitry M, Harris, Midori A, Oliver, Stephen G, Rutherford, Kim, Wood, Valerie, Hayles, Jaqueline, Bähler, Jürg, Bolton, Elizabeth R, De Pons, Jeffery L, Dwinell, Melinda R, Hayman, G Thomas, Kaldunski, Mary L, Kwitek, Anne E, Laulederkind, Stanley JF, Plasterer, Cody, Tutaj, Marek A, Vedi, Mahima, Wang, Shur-Jen, D’Eustachio, Peter, Matthews, Lisa, Balhoff, James P, Aleksander, Suzi A, Alexander, Michael J, Cherry, J Michael, Engel, Stacia R, Gondwe, Felix, and Karra, Kalpana

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Networking and Information Technology R&D (NITRD), Genetics, 1.5 Resources and infrastructure (underpinning), 2.6 Resources and infrastructure (aetiology), Animals, Arabidopsis, Caenorhabditis elegans, Dictyostelium, Drosophila melanogaster, Escherichia coli, Gene Ontology, Humans, Internet, Mice, Molecular Sequence Annotation, Rats, Saccharomyces cerevisiae, Schizosaccharomyces, User-Computer Interface, Zebrafish, Gene Ontology Consortium, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.

Published
2021

10. InterPro in 2017—beyond protein family and domain annotations

Author

Finn, Robert D, Attwood, Teresa K, Babbitt, Patricia C, Bateman, Alex, Bork, Peer, Bridge, Alan J, Chang, Hsin-Yu, Dosztányi, Zsuzsanna, El-Gebali, Sara, Fraser, Matthew, Gough, Julian, Haft, David, Holliday, Gemma L, Huang, Hongzhan, Huang, Xiaosong, Letunic, Ivica, Lopez, Rodrigo, Lu, Shennan, Marchler-Bauer, Aron, Mi, Huaiyu, Mistry, Jaina, Natale, Darren A, Necci, Marco, Nuka, Gift, Orengo, Christine A, Park, Youngmi, Pesseat, Sebastien, Piovesan, Damiano, Potter, Simon C, Rawlings, Neil D, Redaschi, Nicole, Richardson, Lorna, Rivoire, Catherine, Sangrador-Vegas, Amaia, Sigrist, Christian, Sillitoe, Ian, Smithers, Ben, Squizzato, Silvano, Sutton, Granger, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio CE, Wu, Cathy H, Xenarios, Ioannis, Yeh, Lai-Su, Young, Siew-Yit, and Mitchell, Alex L

Subjects
Generic health relevance, Computational Biology, Databases, Protein, Humans, Molecular Sequence Annotation, Phylogeny, Protein Interaction Domains and Motifs, Software, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences.

Published
2017

11. Establishing the ELIXIR Microbiome Community

Author

Finn, Robert D., primary, Balech, Bachir, additional, Burgin, Josephine, additional, Chua, Physilia, additional, Corre, Erwan, additional, Cox, Cymon J., additional, Donati, Claudio, additional, dos Santos, Vitor Martins, additional, Fosso, Bruno, additional, Hancock, John, additional, Heil, Katharina F., additional, Ishaque, Naveed, additional, Kale, Varsha, additional, Kunath, Benoit J., additional, Médigue, Claudine, additional, Pafilis, Evangelos, additional, Pesole, Graziano, additional, Richardson, Lorna, additional, Santamaria, Monica, additional, Van Den Bossche, Tim, additional, Vizcaíno, Juan Antonio, additional, Zafeiropoulos, Haris, additional, Willassen, Nils P., additional, Pelletier, Eric, additional, and Batut, Bérénice, additional

Published
2024
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15. Correction by Construction: Dealing with Drafting Errors by Way of Interpretation

Author

Richardson, Lorna

Subjects
Cultural Studies, History, Law
Abstract

In Monsolar IQ Ltd v Woden Park Ltd1 the Court of Appeal corrected a drafting error in a rent review provision of a lease as part of the interpretive exercise. No claim for rectification of the clause had been made. The Court of Appeal noted that the courts have long been able to disregard the literal meaning of a provision were it is clear (1) that an error has been made; and (2) what the contractual provision should have said. The Court of Appeal was of the view that recent Supreme Court decisions on interpretation had not altered that position.

Published
2023

17. Online Tribes and Digital Authority: What Can Social Theory Bring to Digital Archaeology?

Author

Richardson Lorna-Jane and Lindgren Simon

Subjects
sociology, digital archaeology, social media, theory, archaeological practice, Archaeology, CC1-960
Abstract

From early discussions of the disruptive potential of computer technologies for archaeological applications, to the present era of digital archaeology as the technical underpinning of modern archaeological practice, we have continued to debate the potential impacts of digital communication and digital capture and storage on our knowledge, profession and communications. The increased use of digital tools and methods for archaeological research and dissemination, as well as what Roosevelt (2015) has referred to as the shift to the digital paradigm within archaeological practice, leads us to suggest that the impact of this paradigm shift requires careful and critical examination. This article will examine the edges of the disciplines of archaeology and sociology, where we aim to advance our understanding of the relationship between digital technologies and archaeological knowledge from a uniquely social perspective, using the theoretical approaches of both classic and modern sociologists. The application of this lens of sociology to digital archaeology equips us to understand how archaeology and archaeological practice is situated in a social world, which is especially relevant in the Global West, where digital technology is ubiquitous. Through a critical consideration of the complexity of use of digital technologies within digital archaeology, we can begin to shift our focus away from the character and method of tools and workflow, to the background of intellectual power and influence.

Published
2017
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19. Nonlinear stability analyses for variable viscosity and compressible convection problems

Author

Richardson, Lorna Logan

Subjects
510
Abstract

In this thesis we present nonlinear energy stability analyses of a variety of convection problems, specifically concentrating on compressible convection and convection where the viscosity of the fluid depends on the temperature. To begin we introduce the energy method, which we shall employ in later chapters in order to derive nonlinear stability criteria, and illustrate its effectiveness with a simple one-dimensional example. We then study the stability of a system containing a generalized incompressible fluid, employing linear theory, the energy method and an asymptotic analysis. Next we study a variable viscosity fluid, first establishing continuous dependence of the solution to the Oberbeck-Boussinesq equations, both forward and backward in time, on the viscosity. We then look at convection where the viscosity is first a linear function of the temperature and then a quadratic one. In both cases we employ a generalized energy in order to derive a nonlinear stability boundary. To conclude our analysis of a variable viscosity fluid we also introduce a temperature dependent conductivity and carry out both linear and heuristic nonlinear analyses. We then turn our attention to the phenomenon of convection within a porous medium, concentrating first on penetrative convection. We examine the stability of convection in a porous medium containing an internal heat source and a salt field, using linear theory, the energy method and a weighted energy. Then, returning to the topic of variable viscosity, we demonstrate that, in a porous medium, the solution to the equations of motion depends continuously on the viscosity both forward and backward in time. Finally we study a porous medium saturated with a variable viscosity fluid, employing the Brinkman equation, coupled with the energy method, in order to derive a nonlinear stability boundary.

Published
1993

20. metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data

Author

Zafeiropoulos, Haris, primary, Beracochea, Martin, additional, Ninidakis, Stelios, additional, Exter, Katrina, additional, Potirakis, Antonis, additional, De Moro, Gianluca, additional, Richardson, Lorna, additional, Corre, Erwan, additional, Machado, João, additional, Pafilis, Evangelos, additional, Kotoulas, Georgios, additional, Santi, Ioulia, additional, Finn, Robert D, additional, Cox, Cymon J, additional, and Pavloudi, Christina, additional

Published
2022
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21. MGnify: the microbiome sequence data analysis resource in 2023

Author

Richardson, Lorna, primary, Allen, Ben, additional, Baldi, Germana, additional, Beracochea, Martin, additional, Bileschi, Maxwell L, additional, Burdett, Tony, additional, Burgin, Josephine, additional, Caballero-Pérez, Juan, additional, Cochrane, Guy, additional, Colwell, Lucy J, additional, Curtis, Tom, additional, Escobar-Zepeda, Alejandra, additional, Gurbich, Tatiana A, additional, Kale, Varsha, additional, Korobeynikov, Anton, additional, Raj, Shriya, additional, Rogers, Alexander B, additional, Sakharova, Ekaterina, additional, Sanchez, Santiago, additional, Wilkinson, Darren J, additional, and Finn, Robert D, additional

Published
2022
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25. Metagenomics approach for Polymyxa betae genome assembly enables comparative analysis towards deciphering the intracellular parasitic lifestyle of the plasmodiophorids

Author

UCL - SST/ELI/ELIM - Applied Microbiology, UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Decroës, Alain, Li, Jun-Min, Richardson, Lorna, Mutasa-Gottgens, Euphemia, Lima Mendez, Gipsi, Mahillon, Mathieu, Bragard, Claude, Finn, Robert D., Legrève, Anne, UCL - SST/ELI/ELIM - Applied Microbiology, UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Decroës, Alain, Li, Jun-Min, Richardson, Lorna, Mutasa-Gottgens, Euphemia, Lima Mendez, Gipsi, Mahillon, Mathieu, Bragard, Claude, Finn, Robert D., and Legrève, Anne

Abstract

Genomic knowledge of the tree of life is biased to specific groups of organisms. For example, only six full genomes are currently available in the rhizaria clade. Here, we have applied metagenomic techniques enabling the assembly of the genome of Polymyxa betae (Rhizaria, Plasmodiophorida) RES F41 isolate from unpurified zoospore holobiont and comparison with the A26–41 isolate. Furthermore, the first P. betae mitochondrial genome was assembled. The two P. betae nuclear genomes were highly similar, each with just ~10.2 k predicted protein coding genes, ~3% of which were unique to each isolate. Extending genomic comparisons revealed a greater overlap with Spongospora subterranea than with Plasmodiophora brassicae, including orthologs of the mammalian cation channel sperm-associated proteins, raising some intriguing questions about zoospore physiology. This work validates our metagenomics pipeline for eukaryote genome assembly from unpurified samples and enriches plasmodiophorid genomics; providing the first full annotation of the P. betae genome.

Published
2022

28. List of Contributors

Author

Ahlgren, U., primary, Ahnfelt-Rønne, J., additional, Anderson, Robert H., additional, Armit, Chris, additional, Baldock, Richard, additional, Bard, Jonathan, additional, Brown, Nigel A., additional, Chai, Yang, additional, Davidson, Duncan R., additional, Davies, Jamie, additional, de Castro, Fernando, additional, Dhouailly, Danielle, additional, Eppig, Janan T., additional, Gao, Xia, additional, Gkoutos, Georgios V., additional, Godin, Isabelle, additional, Graham, Elizabeth, additional, Greenfield, Andy, additional, Hayamizu, Terry F., additional, Hill, Robert E., additional, Hoehndorf, Robert, additional, Hogan, Brigid L.M., additional, Hörnblad, A., additional, Kim, Tae-Hee, additional, Lawson, Kirstie A., additional, Lettice, Laura A., additional, López-Mascaraque, Laura, additional, Mallo, Moisés, additional, Mohun, Timothy J., additional, Molnár, Zoltán, additional, Morriss-Kay, Gillian, additional, Moss, Julie, additional, Nord, C., additional, Oftedal, Olav T., additional, Parada, Carolina, additional, Parween, S., additional, Price, David J., additional, Richardson, Lorna, additional, Ringwald, Martin, additional, Roman, Adrianna Katrina San, additional, Sandell, Lisa, additional, Schofield, Paul N., additional, Shivdasani, Ramesh A., additional, Smith, Cynthia L., additional, Sowden, Jane, additional, Streit, Andrea, additional, Thesleff, Irma, additional, Wilson, Valerie, additional, and Wu, Doris K., additional

Published
2016
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29. DH Goes Viral

Author

Barker, Elton, Benardou, Agiatis, Di Giorgio, Sara, Dritsou, Vicky, Dombrowski, Quinn, Felicetti, Achille, Gardikas, Katerina, Garnett, Vicky, Ilvanidou, Maria, Irollo, Alba, Le Floch, Justine, Meghini, Carlo, Mikros, George, Papaki, Eliza, Richardson, Lorna, Schreibman, Susan, Terras, Melissa, and Tsakonas, Giannis

Abstract

As a response to COVID-19 and while the onset of the pandemic was still in its very earlystages, in April 2020 the Digital Curation Unit (DCU), Research and Innovation Center"Athena", as co-ordinator of APOLLONIS, the Greek Infrastructure for Digital Arts, Humanitiesand Language Research and Innovation, organized a Twitter Conference under the title “DHin the Time of Virus”.This event aimed at battling academic isolation and facilitating and supportingcommunity building and osmosis in DH research and education. Due to its sensitive timing,with Italy going through extreme difficulties and Europe and the US entering quarantine andwork-from-home regimes, the Twitter Conference provided a platform of communication of DH research pursuits as well as of expression of an unprecedented human experience. With the support of a DARIAH Theme grant, a year later, in 2021, we designed and organized a digital workshop in which we reunitedthe Twitter Conference participants alongside further DH researchers who were selectedthrough an open call. The outcome of these events is an electronicas well as a printed publication monitoring the effects ofthe pandemic on e-Education, e-Research and digital tools, methods and platforms, thedevelopments the pandemic has expedited and the delays it may have caused in DH researchand the distance covered and toils endured by DH researchers and practitioners to keep trackof their work.

Published
2021
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32. MGnify: the microbiome sequence data analysis resource in 2023.

Author

Richardson, Lorna, Allen, Ben, Baldi, Germana, Beracochea, Martin, Bileschi, Maxwell L, Burdett, Tony, Burgin, Josephine, Caballero-Pérez, Juan, Cochrane, Guy, Colwell, Lucy J, Curtis, Tom, Escobar-Zepeda, Alejandra, Gurbich, Tatiana A, Kale, Varsha, Korobeynikov, Anton, Raj, Shriya, Rogers, Alexander B, Sakharova, Ekaterina, Sanchez, Santiago, and Wilkinson, Darren J

Published
2023
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33. metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data.

Author

Zafeiropoulos, Haris, Beracochea, Martin, Ninidakis, Stelios, Exter, Katrina, Potirakis, Antonis, De Moro, Gianluca, Richardson, Lorna, Corre, Erwan, Machado, João, Pafilis, Evangelos, Kotoulas, Georgios, Santi, Ioulia, Finn, Robert D, Cox, Cymon J, and Pavloudi, Christina

Subjects
GENOMICS, METAGENOMICS, OBSERVATORIES, BIOTIC communities, WORKFLOW, MICROBIAL ecology
Abstract

Background Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner. Findings Based on the established MGnify resource, we developed metaGOflow. metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of 2 EMO BON samples and 1 Tara Oceans sample was performed as a use case. Conclusions metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflow is a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data. [ABSTRACT FROM AUTHOR]

Published
2023
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34. The impact of COVID 19 on service charges in commercial properties

Author

Richardson, Lorna

Subjects
concessions, coronavirus, COVID-19, arrears, commercial lease, service charge
Abstract

This article considers the effect of COVID-19, and the resultant regulations and protective measures that have come into place, on the operation of service charge in commercial properties. The article is in three parts. In the first section, issues in relation to work to common parts and the provision of services are analysed. These issues arise in relation to service charge generally but become especially pertinent in times when commercial tenants are likely to be experiencing cashflow difficulties, with the result that tenants may question and dispute entries in the service charge statement more readily. The second section considers legislative measures that have come into place in response to the pandemic, and examines the effect on the landlord – tenant relationship from a Scots law perspective,i with specific emphasis on the landlord’s ability to recover arrears of service charge. The final section considers non-legislative measures that have a bearing on service charges and their collection in commercial leases.

Published
2021

35. Pfam : The protein families database in 2021

Author

Mistry, Jaina, Chuguransky, Sara, Williams, Lowri, Qureshi, Matloob, Salazar, Gustavo A., Sonnhammer, Erik L. L., Tosatto, Silvio C. E., Paladin, Lisanna, Raj, Shriya, Richardson, Lorna J., Finn, Robert D., Bateman, Alex, Mistry, Jaina, Chuguransky, Sara, Williams, Lowri, Qureshi, Matloob, Salazar, Gustavo A., Sonnhammer, Erik L. L., Tosatto, Silvio C. E., Paladin, Lisanna, Raj, Shriya, Richardson, Lorna J., Finn, Robert D., and Bateman, Alex

Abstract

The Pfam database is a widely used resource for classifying protein sequences into families and domains. Since Pfam was last described in this journal, over 350 new families have been added in Pfam 33.1 and numerous improvements have been made to existing entries. To facilitate research on COVID-19, we have revised the Pfam entries that cover the SARS-CoV-2 proteome, and built new entries for regions that were not covered by Pfam. We have reintroduced Pfam-B which provides an automatically generated supplement to Pfam and contains 136 730 novel clusters of sequences that are not yet matched by a Pfam family. The new Pfam-B is based on a clustering by the MMseqs2 software. We have compared all of the regions in the RepeatsDB to those in Pfam and have started to use the results to build and refine Pfam repeat families. Pfam is freely available for browsing and download at http://pfam.xfam.org/.

Published
2021
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36. Computational strategies to combat COVID-19:useful tools to accelerate SARS-CoV-2 and coronavirus research

Author

Hufsky, Franziska, Lamkiewicz, Kevin, Almeida, Alexandre, Aouacheria, Abdel, Arighi, Cecilia, Bateman, Alex, Baumbach, Jan, Beerenwinkel, Niko, Brandt, Christian, Cacciabue, Marco, Chuguransky, Sara, Drechsel, Oliver, Finn, Robert D., Fritz, Adrian, Fuchs, Stephan, Hattab, Georges, Hauschild, Anne-Christin, Heider, Dominik, Hoffmann, Marie, Hölzer, Martin, Hoops, Stefan, Kaderali, Lars, Kalvari, Ioanna, von Kleist, Max, Kmiecinski, Renó, Kühnert, Denise, Lasso, Gorka, Libin, Pieter, List, Markus, Löchel, Hannah F., Martin, Maria J., Martin, Roman, Matschinske, Julian, McHardy, Alice C., Mendes, Pedro, Mistry, Jaina, Navratil, Vincent, Nawrocki, Eric P., O'Toole, Aíne Niamh, Ontiveros-Palacios, Nancy, Petrov, Anton I., Rangel-Pineros, Guillermo, Redaschi, Nicole, Reimering, Susanne, Reinert, Knut, Reyes, Alejandro, Richardson, Lorna, Robertson, David L., Sadegh, Sepideh, Singer, Joshua B., Theys, Kristof, Upton, Chris, Welzel, Marius, Williams, Lowri, Marz, Manja, Hufsky, Franziska, Lamkiewicz, Kevin, Almeida, Alexandre, Aouacheria, Abdel, Arighi, Cecilia, Bateman, Alex, Baumbach, Jan, Beerenwinkel, Niko, Brandt, Christian, Cacciabue, Marco, Chuguransky, Sara, Drechsel, Oliver, Finn, Robert D., Fritz, Adrian, Fuchs, Stephan, Hattab, Georges, Hauschild, Anne-Christin, Heider, Dominik, Hoffmann, Marie, Hölzer, Martin, Hoops, Stefan, Kaderali, Lars, Kalvari, Ioanna, von Kleist, Max, Kmiecinski, Renó, Kühnert, Denise, Lasso, Gorka, Libin, Pieter, List, Markus, Löchel, Hannah F., Martin, Maria J., Martin, Roman, Matschinske, Julian, McHardy, Alice C., Mendes, Pedro, Mistry, Jaina, Navratil, Vincent, Nawrocki, Eric P., O'Toole, Aíne Niamh, Ontiveros-Palacios, Nancy, Petrov, Anton I., Rangel-Pineros, Guillermo, Redaschi, Nicole, Reimering, Susanne, Reinert, Knut, Reyes, Alejandro, Richardson, Lorna, Robertson, David L., Sadegh, Sepideh, Singer, Joshua B., Theys, Kristof, Upton, Chris, Welzel, Marius, Williams, Lowri, and Marz, Manja

Abstract

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de

Published
2021

42. EMAGE: Electronic Mouse Atlas of Gene Expression

Author

Richardson, Lorna, primary, Stevenson, Peter, additional, Venkataraman, Shanmugasundaram, additional, Yang, Yiya, additional, Burton, Nick, additional, Rao, Jianguo, additional, Christiansen, Jeffrey H., additional, Baldock, Richard A., additional, and Davidson, Duncan R., additional

Published
2013
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44. Towards BioDBcore: a community-defined information specification for biological databases

Author

Gaudet, Pascale, Bairoch, Amos, Field, Dawn, Sansone, Susanna-Assunta, Taylor, Chris, Attwood, Teresa K., Bateman, Alex, Blake, Judith A., Bult, Carol J., Cherry, J. Michael, Chisholm, Rex L., Cochrane, Guy, Cook, Charles E., Eppig, Janan T., Galperin, Michael Y., Gentleman, Robert, Goble, Carole A., Gojobori, Takashi, Hancock, John M., Howe, Douglas G., Imanishi, Tadashi, Kelso, Janet, Landsman, David, Lewis, Suzanna E., Mizrachi, Ilene Karsch, Orchard, Sandra, Ouellette, B. F. Francis, Ranganathan, Shoba, Richardson, Lorna, Rocca-Serra, Philippe, Schofield, Paul N., Smedley, Damian, Southan, Christopher, Tan, Tin Wee, Tatusova, Tatiana, Whetzel, Patricia L., White, Owen, and Yamasaki, Chisato

Published
2011
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45. The InterPro protein families and domains database: 20 years on

Author

Blum, Matthias, primary, Chang, Hsin-Yu, additional, Chuguransky, Sara, additional, Grego, Tiago, additional, Kandasaamy, Swaathi, additional, Mitchell, Alex, additional, Nuka, Gift, additional, Paysan-Lafosse, Typhaine, additional, Qureshi, Matloob, additional, Raj, Shriya, additional, Richardson, Lorna, additional, Salazar, Gustavo A, additional, Williams, Lowri, additional, Bork, Peer, additional, Bridge, Alan, additional, Gough, Julian, additional, Haft, Daniel H, additional, Letunic, Ivica, additional, Marchler-Bauer, Aron, additional, Mi, Huaiyu, additional, Natale, Darren A, additional, Necci, Marco, additional, Orengo, Christine A, additional, Pandurangan, Arun P, additional, Rivoire, Catherine, additional, Sigrist, Christian J A, additional, Sillitoe, Ian, additional, Thanki, Narmada, additional, Thomas, Paul D, additional, Tosatto, Silvio C E, additional, Wu, Cathy H, additional, Bateman, Alex, additional, and Finn, Robert D, additional

Published
2020
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46. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Author

Hufsky, Franziska, primary, Lamkiewicz, Kevin, additional, Almeida, Alexandre, additional, Aouacheria, Abdel, additional, Arighi, Cecilia, additional, Bateman, Alex, additional, Baumbach, Jan, additional, Beerenwinkel, Niko, additional, Brandt, Christian, additional, Cacciabue, Marco, additional, Chuguransky, Sara, additional, Drechsel, Oliver, additional, Finn, Robert D, additional, Fritz, Adrian, additional, Fuchs, Stephan, additional, Hattab, Georges, additional, Hauschild, Anne-Christin, additional, Heider, Dominik, additional, Hoffmann, Marie, additional, Hölzer, Martin, additional, Hoops, Stefan, additional, Kaderali, Lars, additional, Kalvari, Ioanna, additional, von Kleist, Max, additional, Kmiecinski, Renó, additional, Kühnert, Denise, additional, Lasso, Gorka, additional, Libin, Pieter, additional, List, Markus, additional, Löchel, Hannah F, additional, Martin, Maria J, additional, Martin, Roman, additional, Matschinske, Julian, additional, McHardy, Alice C, additional, Mendes, Pedro, additional, Mistry, Jaina, additional, Navratil, Vincent, additional, Nawrocki, Eric P, additional, O’Toole, Áine Niamh, additional, Ontiveros-Palacios, Nancy, additional, Petrov, Anton I, additional, Rangel-Pineros, Guillermo, additional, Redaschi, Nicole, additional, Reimering, Susanne, additional, Reinert, Knut, additional, Reyes, Alejandro, additional, Richardson, Lorna, additional, Robertson, David L, additional, Sadegh, Sepideh, additional, Singer, Joshua B, additional, Theys, Kristof, additional, Upton, Chris, additional, Welzel, Marius, additional, Williams, Lowri, additional, and Marz, Manja, additional

Published
2020
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47. Pfam: The protein families database in 2021

Author

Mistry, Jaina, primary, Chuguransky, Sara, additional, Williams, Lowri, additional, Qureshi, Matloob, additional, Salazar, Gustavo A, additional, Sonnhammer, Erik L L, additional, Tosatto, Silvio C E, additional, Paladin, Lisanna, additional, Raj, Shriya, additional, Richardson, Lorna J, additional, Finn, Robert D, additional, and Bateman, Alex, additional

Published
2020
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50. eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis

Author

Armit, Chris, Richardson, Lorna, Venkataraman, Shanmugasundaram, Graham, Liz, Burton, Nicholas, Hill, Bill, Yang, Yiya, and Baldock, Richard A

Subjects
Internet, Mice, Atlases as Topic, Animals, Embryonic Development, Gene Expression Regulation, Developmental, Cell Biology, Anatomy, Artistic, Embryo, Mammalian, Molecular Biology, Article, Developmental Biology
Abstract

The eMouseAtlas resource is an online database of 3D digital models of mouse development, an ontology of mouse embryo anatomy and a gene-expression database with about 30K spatially mapped gene-expression patterns. It is closely linked with the MGI/GXD database at the Jackson Laboratory and holds links to almost all available image-based gene-expression data for the mouse embryo. In this resource article we describe the novel web-based tools we have developed for 3D visualisation of embryo anatomy and gene expression. We show how mapping of gene expression data onto spatial models delivers a framework for capturing gene expression that enhances our understanding of development, and we review the exploratory tools utilised by the EMAGE gene expression database as a means of defining co-expression of in situ hybridisation, immunohistochemistry, and lacZ-omic expression patterns. We report on recent developments of the eHistology atlas and our use of web-services to support embedding of the online ‘The Atlas of Mouse Development’ in the context of other resources such as the DMDD mouse phenotype database. In addition, we discuss new developments including a cellular-resolution placental atlas, third-party atlas models, clonal analysis data and a new interactive eLearning resource for developmental processes., Highlights • 3D Atlas models enable detailed understanding of mouse embryo anatomy. • Point clouds facilitate enhanced visualisation of coexpression. • Database queries allow gene expression patterns to be analysed spatially in relation to each other. • Web-services enable Atlas support for phenotyping studies.

Published
2017
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