standOff. When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote shown on the same row, so the borrowing can be checked against the thing borrowed from without leaving this page. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.| relation to other work | claim_relations | how this paper stands to another: agrees, contradicts, extends, qualifies |
| claim type | claim_type | the shape of the claim: existence, mechanism, method, critique, prediction, null |
| concept edge | concept_edges | an asserted relation between two concepts, with the sentence asserting it |
| concept | concepts | an idea the paper works with, quoted where the paper uses it |
| content tag | content_tags | a finding, definition, quantity, statistic or variable named in the paper |
| contribution | contribution | what the paper claims to add |
| control | controls | an experiment run to eliminate a rival explanation |
| limitation | limitations | what the paper says its evidence cannot support |
| mechanism | mechanisms | how the reported effect is said to come about |
| method | method | how the paper produced its evidence |
| object of study | object_of_study | what the paper is about — the thing it investigates |
| phenomenon | phenomenon | the effect or regularity under study |
| research question | research_question | the question the paper sets itself |
| sense | senses | a distinct use of a term, quoted where the paper fixes it |
The reference list is not part of the text we hold for this paper. Our copy was extracted from the publisher's page and the bibliography did not survive that extraction, so the article below ends before its references. Nothing has been removed by us.
Abstract. Abstract The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site ( http://ictv.global ) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report ( http://ictv.global/report/ ), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. content_tagsNo other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy. INTRODUCTION concepts↗concepts↗sensesclaim_relationsconcept_edgescontent_tags↗The process used to study any new biological entity begins by classifying it in relation to other known biological organisms, and then giving it a name ( 1 – 3 ). This process of classification and naming comprises the discipline of taxonomy, and has been an integral part of biological research since at least the 18th Century when Carl Linnaeus defined the principles of modern taxonomy ( 4 ). Taxonomic classification is a scientific endeavor whereby biological organisms are grouped together and placed into their proper taxonomic hierarchy based on the characteristics that form a unique descriptor identifying a particular organism. limitationscontent_tagsThis research process is driven by individual scientists who publish their work, providing their evidence for the proposed classification. As new data are obtained either on the organisms previously studied, or on related organisms, the classification hierarchy may change. content_tagsThe principles, procedures, and nomenclature used to name taxa, is handled by one of the international organizations charged with developing the necessary guidelines. For example, naming of animal species is subject to the principles established by the International Commission on Zoological Nomenclature ( 2 , 5 ). Naming of bacterial species is guided by the International Committee on Systematic Bacteriology ( 3 ). The taxonomic classification of viruses and naming of virus taxa is the responsibility of the International Committee on Taxonomy of Viruses (ICTV) ( 6 ). The ICTV is charged with the task of developing, refining, and maintaining a universal virus taxonomy by the Virology Division of the International Union of Microbiological Societies ( 7 ). research_questionmechanismsconcepts↗concepts↗concept_edgescontent_tagsUnlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomy and names before they become official. concepts↗concepts↗claim_relationsconcept_edgescontent_tagsThe rules governing the ICTV and its operations are defined by the ICTV Statutes ( http://ictv.global/statutes.asp ), while the rules for creating and naming virus taxa are provided in the International Code of Virus Classification and Nomenclature ( http://ictv.global/codeOfVirusClassification.asp ). concepts↗concepts↗sensesconcept_edgescontent_tagscontent_tagsThe ICTV was established in 1966 as the International Committee on Nomenclature of Viruses, and was renamed the International Committee on Taxonomy of Viruses in 1977 ( 6 , 8 , 9 ). The ICTV consists of a series of officers, subcommittee chairs, and elected members that oversee taxonomic classification and naming. There are six subcommittees, each of which covers a different group of viruses, differentiated by the type of host the virus infects (animal, plant, fungal and protist, or bacterial and archaeal) and the molecular composition of the virus genome (DNA, RNA, double or single stranded and translational polarity). limitationscontrolsconcepts↗concepts↗concepts↗concept_edgescontent_tagscontent_tags↗content_tags↗Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria for classification and naming. These demarcation criteria are based upon the genetic and biological properties of the taxon members, and cover each of the taxonomic ranks currently recognized by the ICTV: order, family, subfamily, genus and species. In addition to overseeing taxonomic decisions, the ICTV is also charged with disseminating these decisions to the scientific community. Therefore, the ICTV maintains a database that stores the virus taxonomy, taxon names, and associated metadata, including information on exemplar viruses for each named species. The ICTV web site ( http://ictv.global ) provides access to its taxonomy database and also provides an extensive collection of information supporting its overall activities, including the ICTV Report that provides a complete description of every defined virus taxon. DATABASE AND WEB SITE Virus classification sensescontent_tagsClassification of viruses is based on the collection and comparison of various characters that describe the virus, and can then be used to distinguish one virus from another ( 1 , 10 – 15 ). Characters can consist of any property or feature of the virus, and include the molecular composition of the genome; the structure of the virus capsid and whether or not it is enveloped; the gene expression program used to produce virus proteins; host range; pathogenicity; and sequence similarity. While all characters are important in determining taxonomic relationships, sequence comparisons using both pairwise sequence similarity and phylogenetic relationships have become one of the primary sets of characters used to define and distinguish virus taxa. concepts↗concepts↗concept_edgescontent_tagsBased on an assessment of characters, a hierarchical relationship is established that groups together viruses with similar properties. The properties that define higher-level taxa are shared with all lower-level taxa that belong to higher-level taxa ( 15 ). For example, viruses of the order Picornavirales all are non-enveloped, icosahedral particles containing one or two segments of positive-sense RNA ( 16 ). The family Picornaviridae is one of (currently) five families belonging to the order Picornavirales . Members of the family Picornaviridae contain a single monocistronic genome with conserved genome organization (arrangement of encoded polypeptides). limitationscontent_tagscontent_tagsMembers of the genus Enterovirus (family Picornaviridae ) share more than 42% amino acid identity across the length of their polyprotein. Finally, members of the species Enterovirus C , share a limited range of hosts and host receptors, have similar polyprotein processing programs, and share more than 70% amino acid identity in the polyprotein. Once these criteria for grouping similar viruses into common taxa are established, they are used as demarcation criteria to determine if newly discovered viruses are members of an existing species (and therefore also in existing higher-level taxa), or if the new viruses warrant creation of a new species (and potentially new higher-level taxa), if their properties are sufficiently distinct from the viruses in an existing species. The ICTV database of virus taxonomy object_of_studymethod↗mechanismscontrolscontent_tagsEvery year, virologists submit proposals to the ICTV recommending the creation of new taxa as well as renaming, moving, or abolishing existing taxa. These proposals are submitted to the appropriate study group which then evaluates and modifies the proposal as necessary, in consultation with the original author. Once a year, the ICTV Executive Committee (EC) meets, discusses all submitted proposals, and will either accept a proposal, send it back for modification, or reject it. Then the set of accepted proposals are sent to the ICTV membership for ratification. Once ratified, the newly approved taxonomy is entered in the ICTV taxonomic database. The database utilizes a relational schema built using Microsoft SQL Server. claim_typephenomenonmechanismsconcepts↗sensescontent_tagscontent_tags↗content_tagsThe tables store a controlled vocabulary used for specific fields where the possible data values remain fairly constant. These include taxonomy level (currently species, genus, subfamily, family, and order), possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish), and virus genome type (e.g. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(–), etc.) that forms part of the annotation available for the member viruses of each species. contributionmechanismscontrolscontent_tagsEach record in the taxonomy table stores data on a single taxon including its name, numerical id, parent taxon, release number and date, most recent taxonomic change, filename of the proposal establishing the taxon, and a pointer to its previous record if a change has occurred in taxon data (such as moving a species to another genus). With this information, a complete history of every taxon can be reconstructed from the database. Table 1 displays an example set of database records for the species Measles morbillivirus . Table 1. Database Records for the Species Measles morbillivirus Table Field Record 1 Record 2 taxon_name Measles virus Measles morbillivirus taxon_level Species Species release_number 30 31 release_year 2015 2016 taxon_id (stable) 19750163 19750163 node_id (new with each release) 20151044 20161044 parent_taxon Morbillivirus Morbillivirus last_change move rename proposal 2015.011a-iM.A.v2.Pneumoviridae.pdf 2016.011aM.A.v2.Paramyxoviridae_spren.pdf The two most recent records in the ICTV database are displayed, detailing changes in the taxonomic classification and naming of virus members of this species. Data stored in the taxonomy database can be accessed visually from the ICTV web site ( http://ictv.global/virusTaxonomy.asp ) using the taxonomy browser: a hierarchical series of expandable, tabular rows, with each row containing information on a single taxon (Figure 1 ). Each taxon is presented in its proper position in the taxonomic hierarchy (Figure 2 ). Each row is labeled with the number of lower-level taxa belonging to each higher-level taxon, and a link is provided to the complete history of each taxon (see below). A search box is available to search the current, or current and historical taxonomy releases for any taxon that includes the text entered in the search box ( Supplementary Figure S1 ). Each search result is linked to the identified taxon in the hierarchical taxonomy browser. Figure 1. Taxonomy Web Page. A screen shot of the ICTV web page ( http://ictv.global/virusTaxonomy.asp ) that contains the taxonomy browser and search form. Figure 2. Taxonomy browser. The online taxonomy browser, showing an expanded view of the taxonomic hierarchy of the species Measles morbillivirus . The ‘history’ links to the right of each row are colored green if there has been a change in the indicated taxon since the last release. Clicking on any ‘history’ link will take the user to the taxon history page (Figure 3 ). The complete taxonomy for any one release (the Master Species List) is also available for download as an Excel spreadsheet ( http://ictv.global/msl.asp ). These spreadsheets are available for every release back to 2008. Each new taxonomy release is also shared with the National Center for Biotechnology Information (NCBI) of the National Institutes of Health so that the taxonomy database they maintain and use for the annotation of virus sequence records can be kept up-to-date with the most recent ICTV taxonomy. Historical taxonomy releases The ICTV database contains the complete taxonomy for every release since the taxonomy was first produced in 1971 (Table 2 ) ( 6 , 8 ). Each of these releases can be accessed using the taxonomy browser by following the appropriate link on the release history web page ( http://ictv.global/taxonomyReleases.asp ). In addition, by selecting the ‘history’ link from the taxonomy browser (Figure 2 ), a page displaying the complete history of the selected taxon is displayed (Figure 3 ). This history is constructed from the complete set of database records that are part of the historical path leading to the selected taxon, and to the most recent child of that taxon in the last release recording a change. For example, in Figure 3 , limitationscontrolscontent_tagsthe most recent change to this particular taxonomic lineage was the creation of the species Alphacoronavirus 1 in 2009. But in fact, this was not a new species, but was a merging of three existing species (transmissible gastroenteritis virus, feline coronavirus, and canine coronavirus) into one, newly renamed species, Alphacoronavirus 1 . In addition, the species were moved from the now defunct genus coronavirus, into the genus Alphacoronavirus that is a member of the subfamily Coronavirinae . This particular history goes back to the first ICTV data release in 1971 when the species transmissible gastro-enteritis virus of swine was created as a member of the genus coronavirus. (The species concept in virus taxonomy was not defined until 1996 ( 8 ). Therefore any ‘species’ present in the database between 1971 and 1995 represents an informal taxonomic rank, existing to contain the viruses that are members of each genus and higher-level ranks.) Table 2. Taxonomy Release History. Information on each release of the approved ICTV taxonomy is displayed including the date and location of the ICTV meeting where proposals were discussed; the Master Species List (MSL) release number and the number of taxa belonging to each taxon rank present in the ICTV database for the indicated release Number of Taxa Year Release Information Order Family Subfamily Genus Species 2016 EC 48, Budapest, Hungary, August 2016; Email ratification 2017 (MSL #31) 8 122 35 735 4404 2015 EC 47, London, UK, July 2015; Email ratification 2016 (MSL #30) 7 111 27 609 3704 2014 EC 46, Kingston and Montreal, Canada, July 2014, Email ratification 2015 (MSL #29) 7 104 23 505 3185 2013 EC 45, Edinburgh, July 2013; Email ratification 2014 (MSL #28) 7 103 22 455 2827 2012 EC 44, Leuven, July 2012; Email ratification 2013 (MSL #27) 7 96 22 420 2617 2011 EC 42: Paris, June 2010; EC43: Sapporo, September 2011; Email ratification 2012 (MSL #26) 6 94 22 395 2480 2009 ICTV 9th Report; EC41: Leiden, June 2009; Email ratification 2009 (MSL #25) 6 87 19 349 2285 2008 EC 39: Kingston, June 2007; EC 40: Istanbul, August 2008; Email ratification 2008 (MSL #24) 5 82 11 307 2079 2005 ICTV 8th Report (MSL #23) 3 73 11 289 1899 2004 Postal vote 2004 (MSL #22) 3 73 11 290 1832 2002 Plenary session, July 2002, Paris (MSL #21) 3 70 11 251 1619 2002 Postal vote spring 2002 (MSL #20) 3 70 9 247 1602 1999 Plenary session, August 1999, Sydney (MSL #19) 3 64 9 239 1550 1999 ICTV 7th Report (MSL #18) 3 64 9 234 1551 1998 Postal vote autumn 1998 (MSL #17) 3 63 9 233 2370 1997 Postal vote autumn 1997 (MSL #16) 2 56 9 197 2267 1996 Plenary session, August 1996, Jerusalem (MSL #15) 2 53 9 182 2253 1995 ICTV 6th Report (MSL #14) 1 50 9 166 2220 1993 Plenary session, August 1993, Glasgow (MSL #13) 1 49 9 160 1700 1991 ICTV 5th Report (MSL #12) 1 40 9 142 1674 1990 Plenary session, August 1990, Berlin (MSL #11) 1 40 9 137 1290 1987 Plenary session, August 1987, Edmonton (MSL #10) 0 37 8 116 1275 1984 Plenary session, September 1984, Sendai (MSL #09) 0 35 8 103 1222 1982 ICTV 4th Report (MSL #08) 0 29 8 97 1209 1981 Plenary session, August 1981, Strasbourg (MSL #07) 0 29 8 93 1091 1979 ICTV 3rd Report (MSL #06) 0 24 8 84 1008 1978 Plenary session, August 1978, The Hague (MSL #05) 0 24 7 76 760 1976 ICTV 2nd Report (MSL #04) 0 17 3 67 754 1975 Plenary session, September 1975, Madrid (MSL #03) 0 17 1 63 309 1974 Postal vote April-May 1974 (MSL #02) 0 5 0 49 298 1971 ICTV 1st Report (MSL #01) 0 2 0 43 290 Figure 3. Taxon history. Complete history of the species Alphacoronavirus 1 . The bottom of the figure displays the earliest taxon (transmissible gastro-enteritis virus of swine) into which viruses belonging to the current taxon, Alphacoronavirus 1 , were classified. Moving up the page provides an account of every change that has occurred including moves to new higher-level taxa, new names, and merges with other existing species. Within a particular release, a grayed-out row indicates that there was no change to that taxon, while other rows depict changes as indicated by the label above the row (New, Moved, Renamed and Merged). Each change indicated in the historical taxonomic record is documented by the taxonomy proposal that was submitted to the ICTV proposing that change. These proposals are accessible from the ICTV web site, and can be downloaded as pdf files ( Supplementary Figure S2 ). Links to each relevant proposal are provided from the taxonomy history web page (Figure 3 ). Proposals are available for all taxonomic changes since 2008; though many earlier proposals are also available. ICTV Online (10th) Report on virus taxonomy In addition to providing current and historical access to the ICTV taxonomy through the web-based browser and the Master Species List, the ICTV has also published a compendium, the ‘ICTV Reports on Virus Taxonomy: The Classification and Nomenclature of Viruses’ since 1971, providing a description of all virus taxa existing at the time of publication ( 1 , 9 , 17 , 18 ). This has been published as a hard-copy book, and contains a complete listing of all taxa, along with a list of exemplar viruses corresponding to each species. In addition, these reports provide extensive information on each taxon, describing the properties and characteristics of the virus members of each taxon. These reports also contain a description of the demarcation criteria used to determine whether a particular virus should be classified into an existing species, or whether the creation of a new species (and potentially higher-level taxa) is warranted. The last hard-copy ICTV Report published was the ninth Report, published in 2012 ( 1 ). (Due to the length of time required to compile the report, the ninth Report was based on the 2009 ICTV taxonomy release.) The ninth report is currently available as an open-source publication from the ICTV web site ( http://ictv.global/9th-report/ ). The ICTV 10th Report on Virus Taxonomy is being published in an online format, and is available from the ICTV web site ( http://ictv.global/report/ ). The 10th report is being published sequentially as chapters are released at the rate of ∼25 a year. Report chapters provide a thorough description of each virus taxon, and are generally organized by taxonomic family (Figure 4 ). Within each family, separate sections describe each genus and the member species of that genus. Each of these sections contains a member species table that provides a list of species, and one exemplar virus corresponding to that species. These exemplars are not meant to be a comprehensive listing of all member viruses of the species, but comprise viruses that can serve as a prototypic member of each species. These tables are populated from information stored within the ICTV database, and may also provide names of additional prototypic virus isolates, as well as accession number-based links to available GenBank ( 19 ) sequence records ( Supplementary Table S1 ). Accession numbers for RefSeq ( 20 ) sequence records are also stored in the database and will be made available in a future update of the web site. Figure 4. ICTV Report chapter. A screen shot of the web page depicting the Flaviviridae chapter of the ICTV Online (10th) Report ( http://ictv.global/report/flaviviridae/ ). In addition to the Online Report, the ICTV is also partnering with the Journal of General Virology to publish short summaries of each report chapter ( 21 ). These ICTV Virus Taxonomy Profiles are published at the same time as the Online Report chapters, and consist of a two to three-page review of the properties of each virus family. These profiles serve as citable references for the Online Report chapters ( 22 ). FUTURE DEVELOPMENTS A number of challenges currently exist for the ICTV and virus taxonomy that generally derive from our nascent understanding of the true extent of worldwide virus diversity, arising from new and more efficient technologies for discovering, measuring, and characterizing that diversity ( 10 , 23 – 29 ). Virus discovery has been one of the areas of emphasis of large environmental sampling and metagenomic sequencing projects. The goal of these projects is to more thoroughly assess, in an unbiased manner, the true diversity of biological organisms in a particular environment at a particular place in time, by sequencing the genomes of all organisms present in a sample using high-throughput sequencing technologies. For viruses, this entails utilizing methods that sequence not only DNA-based organisms, but organisms (viruses) with RNA genomes, by including a reverse transcription step in the metagenomic isolation and sequencing pipeline. Once the sequence reads have been generated, efficient sequence assemblers are then able to then identify the reads unique to a single virus genome, and assemble them into a complete, or almost complete, genomic sequence. These metagenomic sequencing projects have resulted in the assembly of thousands of new virus genomes that when classified, should result in the creation of thousands of new virus species and higher-level taxa. In June of 2016, the ICTV helped organize a meeting to discuss metagenomic sequencing and its impact on virus classification. A consensus statement published by meeting participants recommended that viruses detected solely by metagenomic sequencing contain sufficient information in their genomic sequence to support their classification and naming ( 30 , 31 ). The ICTV concurred with that recommendation. Therefore, the ICTV is now accepting proposals for new virus taxa supported solely by metagenomic sequence information. This policy should ensure that the official ICTV virus taxonomy will be much more reflective of the true diversity of existing viruses. But at the same time, this will require that the systems in place for characterizing virus diversity, proposing new virus taxa, storing these taxa in the ICTV database, and browsing and searching for these taxa from the ICTV web pages, be streamlined and made capable of handling the many thousands of new taxa that will need to be created. The ICTV may also need to modify its policies and procedures for naming of virus species and expand the available taxonomic ranks needed to classify these viruses, to handle the large number of new, diverse viruses discovered using metagenomic sequencing methods. In the past, the ICTV has continually modified and modernized its approach to virus taxonomy through, for example, moving to sequence-based characters as the primary source of information needed for classification ( 30 ); developing and utilizing automated computational methods to facilitate the grouping of viruses into taxa (existing and new) based on a comparison of their genomic sequences ( 10 , 32 – 35 ); operating more efficiently and shortening the time taken to approve proposals for new taxa; and now, basing taxonomic decisions solely on the information contained in genomic sequences ( 30 ). It is only through this process of continued evaluation of the current state of virus discovery and research, responding to new data and new understanding by updating policies and procedures, that the ICTV will be able to remain current and continue to be relevant to the scientific community. AVAILABILITY The ICTV web site and all applications accessing the ICTV database are available from http://ictv.global/ . The database and web site are the responsibility of the ICTV Data Secretary, an elected position of the ICTV membership serving a 6-year term. This position, and the provision of the database and web site are defined within and required by the ICTV Statutes ( http://ictv.global/statutes.asp ), thus assuring the long-term existence of this resource. Unless otherwise noted, all information provided by the ICTV from its web site are provided under the Creative Commons Attribution-ShareAlike 4.0 International license ( https://creativecommons.org/licenses/by-sa/4.0/ ). Supplementary Material Supplementary Data Click here for additional data file. ACKNOWLEDGEMENTS We would like to acknowledge the assistance and support of the entire ICTV Executive Committee, and the extensive work of the ICTV Study Group chairs and members, for their work preparing and reviewing taxonomy proposals, and in preparing the Online (10th) Report chapters. SUPPLEMENTARY DATA Supplementary Data are available at NAR online. FUNDING The ICTV is supported by a grant from the Wellcome Trust [WT108418AIA]; contributions from the Virology Division of the International Union of Microbiological Societies, the American Society of Virology, and the Microbiology Society; and support from Archives of Virology. Funding for open access charge: Department of Microbiology, University of Alabama at Birmingham (to E.J.L.). Conflict of interest statement . None declared.
Relations on this page carry a quotation for the claim. Where a relation was separately evidenced — and so tested against the vocabulary for its type — the row says so; none of 6 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.
| facet | tag | field | conf. | whose words |
|---|---|---|---|---|
| object_of_study | A CONTROLLED VOCABULARY WITH A PUBLISHED CONSTITUTION - the virus taxonomy, its governing committee, its two rulebooks, its annual proposal-to-ratification cycle, and a database that records every change back to 1971 | object_of_study | the paper's words | |
| research_question | how the universal virus taxonomy is developed, approved, recorded and made available | research_question | the paper's words | |
| contribution | a description of the ICTV taxonomy database and web site, its schema, its change vocabulary and its complete taxon history | contribution | the paper's words | |
| claim_type | method | claim_type | the paper's words | |
| phenomenon | a scientific vocabulary that changes every year by vote, whose changes are typed and stored rather than left to be reconstructed from the literature | phenomenon | the paper's words | |
| method | system-or-tool-building also in: system-or-tool-building | method | the paper's words | |
| mechanisms | A CONTROLLED VOCABULARY OF CHANGES TO A CONTROLLED VOCABULARY, IN A DATABASE COLUMN: `possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish)`. SIX OPERATIONS. This project has been reconstructing that list by hand from macdonald2015, welsh2024, larson2015 and leask2012; virology has had it as an enumerated field since the taxonomy's first release | mechanisms[0] | 0.95 | the tagger's words |
| mechanisms | AND THE HISTORY IS RECONSTRUCTABLE BY DESIGN: each record stores `release number and date, most recent taxonomic change, filename of the proposal establishing the taxon, and a pointer to its previous record if a change has occurred ... With this information, a complete history of every taxon can be reconstructed from the database`. The proposal that made the change is named in the row | mechanisms[1] | 0.95 | the tagger's words |
| mechanisms | THE GOVERNANCE IS A PUBLISHED PROCEDURE: `Every year, virologists SUBMIT PROPOSALS ... recommending the creation of new taxa as well as renaming, moving, or abolishing existing taxa ... the ICTV Executive Committee meets, discusses all submitted proposals, and will either ACCEPT a proposal, SEND IT BACK for modification, or REJECT it. Then the set of accepted proposals are sent to the ICTV membership FOR RATIFICATION` | mechanisms[2] | 0.95 | the tagger's words |
| mechanisms | and virology is unusual in giving one body BOTH powers: `Unlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification of viruses, and approving the proposed taxonomy and names before they become official`. Zoology and bacteriology separate the naming rules from the classification decision; virology does not | mechanisms[3] | 0.95 | the tagger's words |
| limitations | THE DEMARCATION CRITERIA ARE WRITTEN BY THE PEOPLE WHO APPLY THEM, BY DESIGN: `Each subcommittee contains a series of study groups, generally one per virus family, that develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria`. One committee per family writes the rule and judges the application - `the definer never fixes their own terms`, institutionalised | limitations[0] | 0.95 | the tagger's words |
| limitations | AND ONE OF THOSE CRITERIA IS A BARE PERCENTAGE: `members of the genus Enterovirus share MORE THAN 42% AMINO ACID IDENTITY across the length of their polyprotein`. No derivation is offered for 42, and the sentence stating it carries no definitional language at all - it is a fact about members, doing the work of a criterion | limitations[1] | 0.95 | the tagger's words |
| limitations | AND THE CHANGE TYPE STORED CAN MISREPRESENT THE CHANGE: `the most recent change ... was the creation of the species Alphacoronavirus 1 in 2009. But in fact, this was not a new species, but was a merging of three existing species ... into one, newly renamed species ... In addition, the species were moved from the now defunct genus coronavirus`. THREE OF THE SIX OPERATIONS AT ONCE, RECORDED AS ONE, and the paper has to say `but in fact` to correct its own database | limitations[2] | 0.85 | the tagger's words |
| limitations | and the hierarchy is expected to move: `As new data are obtained either on the organisms previously studied, or on related organisms, the classification hierarchy may change`. A vocabulary that is correct at a release number rather than simply correct | limitations[3] | 0.95 | the tagger's words |
| controls | annual Executive Committee review followed by ratification by the whole membership eliminates: a single study group's criteria becoming official without scrutiny - the EC 'will either accept a proposal, send it back for modification, or reject it', and only then does the membership ratify · outcome: held | controls[0] | 0.95 | the tagger's words |
| controls | a stored 'previous record' pointer and the filename of the proposal that made each change eliminates: the loss of a taxon's history when its name or parent changes - 'a complete history of every taxon can be reconstructed from the database' · outcome: held | controls[1] | 0.95 | the tagger's words |
| controls | whether the stored change type describes the change that happened eliminates: nothing, and the paper's own worked example shows it: a record of 'creation' that 'in fact ... was not a new species, but was a merging of three existing species ... into one, newly renamed species' that was also moved to a different genus · outcome: failed | controls[2] | 0.85 | the tagger's words |
| controls | whether the demarcation criteria are set independently of the people applying them eliminates: nothing - it is the design: study groups 'develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria' · outcome: failed | controls[3] | 0.95 | the tagger's words |
| concepts | controlled vocabulary also in: controlled vocabulary | concepts[0] | 0.95 | the paper's words |
| concepts | International Committee on Nomenclature of Viruses | concepts[1] | 0.95 | the paper's words |
| concepts | International Committee on Taxonomy of Viruses | concepts[2] | 0.95 | the paper's words |
| concepts | ICTV Statutes also in: ICTV Statutes | concepts[3] | 0.95 | the paper's words |
| concepts | International Code of Virus Classification and Nomenclature | concepts[4] | 0.95 | the paper's words |
| concepts | demarcation criteria also in: demarcation criteria | concepts[5] | 0.95 | the paper's words |
| concepts | study groups also in: study groups | concepts[6] | 0.95 | the paper's words |
| concepts | subcommittee also in: subcommittee | concepts[7] | 0.95 | the paper's words |
| concepts | classification and naming also in: classification and naming | concepts[8] | 0.95 | the paper's words |
| concepts | taxonomy also in: taxonomy | concepts[9] | 0.95 | the paper's words |
| concepts | lower-level taxa also in: lower-level taxa | concepts[10] | 0.95 | the paper's words |
| concepts | higher-level taxa also in: higher-level taxa | concepts[11] | 0.95 | the paper's words |
| concepts | ICTV also in: ICTV | concepts[12] | 0.95 | the paper's words |
| concepts | other groups of biological organisms also in: other groups of biological organisms | concepts[13] | 0.95 | the paper's words |
| senses | `taxonomic change` - AN ENUMERATED TYPE WITH SIX VALUES: `new, split, move, merge, rename, and abolish`. Not prose, not a convention - a controlled field in a SQL schema, stored per taxon per release | senses[0] | 0.95 | the tagger's words |
| senses | `taxonomy` AS A DISCIPLINE - `This process of classification and naming comprises the discipline of taxonomy`. Two acts, one discipline, and the ICTV is unusual in holding authority over both | senses[1] | 0.95 | the tagger's words |
| senses | `character` - `any property or feature of the virus`, including genome composition, capsid structure, envelopment, gene expression programme, HOST RANGE, PATHOGENICITY and sequence similarity. AND ONE FAMILY OF CHARACTERS HAS WON: `sequence comparisons ... have become one of the primary sets of characters used to define and distinguish virus taxa` | senses[2] | 0.95 | the tagger's words |
| senses | `ICTV` - the committee, which RENAMED ITSELF FROM NAMING TO CLASSIFYING: `established in 1966 as the International Committee on NOMENCLATURE of Viruses, and was RENAMED the International Committee on TAXONOMY of Viruses in 1977` | senses[3] | 0.95 | the tagger's words |
| claim_relations | extends → Linnaean taxonomy, named in the paper as the origin of the principles, applied to entities that are not organisms | claim_relations[0] | 0.95 | the tagger's words |
| claim_relations | supports → the position that a scientific vocabulary needs a governing body, a written code and a versioned record - the ICTV has all three and the paper describes each | claim_relations[1] | 0.95 | the tagger's words |
| concept_edges | International Committee on Nomenclature of Viruses —renamed-across-fields→ International Committee on Taxonomy of Viruses strength of the relation: 0.95 · note: THE REMIT CHANGED WITH THE NAME: from NOMENCLATURE to TAXONOMY in 1977, and the paper's next claim is that this committee, unlike its counterparts in zoology and bacteriology, also approves each classification
Audit 2026-09-28: DOUBTFUL - read against its span and kept, but a committee renamed itself; renamed-across-fields overstates a renaming within one body. | concept_edges[0] | 0.95 | the tagger's words |
| concept_edges | ICTV —contrasted-with→ other groups of biological organisms strength of the relation: 0.95 · note: 'the ICTV charge extends NOT ONLY to developing the guidelines for naming of taxa, BUT to establishing guidelines for taxonomic classification, AND APPROVING the proposed taxonomy and names before they become official'. One body writes the rules and rules on each application also in: ICTV · other groups of biological organisms | concept_edges[1] | 0.95 | the tagger's words |
| concept_edges | ICTV Statutes —distinct-from→ International Code of Virus Classification and Nomenclature strength of the relation: 0.95 · note: one document governs the COMMITTEE, the other governs the TAXA. A vocabulary with a constitution and a style guide, kept separate | concept_edges[2] | 0.95 | the tagger's words |
| concept_edges | study groups —part-of→ subcommittee strength of the relation: 0.95 · note: generally one study group per virus family, and the study group both writes the demarcation criteria and evaluates proposals against them also in: study groups · subcommittee | concept_edges[3] | 0.95 | the tagger's words |
| concept_edges | lower-level taxa —part-of→ higher-level taxa strength of the relation: 0.95 · note: 'The properties that define higher-level taxa are shared with all lower-level taxa that belong to higher-level taxa' - definitional inheritance, stated as the rule rather than as a fact about any particular pair also in: lower-level taxa · higher-level taxa | concept_edges[4] | 0.95 | the tagger's words |
| concept_edges | classification and naming —part-of→ taxonomy strength of the relation: 0.95 · note: 'This process of classification and naming comprises the discipline of taxonomy' - two acts, one discipline, and the ICTV is unusual in holding authority over both
Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span says classification and naming COMPRISES the discipline of taxonomy; part-of is loose. also in: classification and naming · taxonomy | concept_edges[5] | 0.95 | the tagger's words |
| content_tags | A CONTROLLED VOCABULARY OF CHANGES TO A CONTROLLED VOCABULARY, IN A DATABASE COLUMN: `possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish)`. SIX OPERATIONS, ENUMERATED AND STORED PER TAXON PER RELEASE | content_tags.findings[0] | 0.95 | the tagger's words |
| content_tags | AND THE HISTORY IS RECONSTRUCTABLE BY DESIGN: each row stores the release, the change type, `the filename of the proposal establishing the taxon, and A pointer to its previous record` - so `a complete history of every taxon can be reconstructed from the database` | content_tags.findings[1] | 0.95 | the tagger's words |
| content_tags | A WORKED EXAMPLE OF THREE OPERATIONS RECORDED AS ONE: `the creation of the species Alphacoronavirus 1 in 2009. But in fact, this was not a new species, but was a merging of three existing species ... into one, newly renamed species ... the species were moved from the now defunct genus coronavirus` | content_tags.findings[2] | 0.85 | the tagger's words |
| content_tags | THE COMMITTEE RENAMED ITSELF FROM NAMING TO CLASSIFYING: `established in 1966 as the International Committee on NOMENCLATURE of Viruses, and was RENAMED the International Committee on TAXONOMY of Viruses in 1977` | content_tags.findings[3] | 0.95 | the tagger's words |
| content_tags | AND VIROLOGY GIVES ONE BODY BOTH POWERS: `Unlike for other groups of biological organisms, the ICTV charge extends not only to developing the guidelines for naming of taxa, but to establishing guidelines for taxonomic classification ... and approving the proposed taxonomy and names before they become official` | content_tags.findings[4] | 0.95 | the tagger's words |
| content_tags | TWO SEPARATE RULEBOOKS: the `ICTV Statutes` govern the committee, the `International Code of Virus Classification and Nomenclature` governs the taxa | content_tags.findings[5] | 0.95 | the tagger's words |
| content_tags | THE GOVERNANCE IS AN ANNUAL PUBLISHED PROCEDURE: proposals from virologists, evaluation by the study group `in consultation with the original author`, an Executive Committee decision to `accept ... send it back ... or reject`, then `RATIFICATION` by the membership | content_tags.findings[6] | 0.95 | the tagger's words |
| content_tags | THE DEMARCATION CRITERIA ARE WRITTEN BY THE PEOPLE WHO APPLY THEM, BY DESIGN: study groups `develop the demarcation criteria used to define each new taxon, and evaluate proposals using those criteria` | content_tags.findings[7] | 0.95 | the tagger's words |
| content_tags | AND ONE CRITERION IS A BARE PERCENTAGE: `members of the genus Enterovirus share MORE THAN 42% AMINO ACID IDENTITY across the length of their polyprotein` - no derivation, and the sentence carries no definitional language | content_tags.findings[8] | 0.95 | the tagger's words |
| content_tags | ONE FAMILY OF CHARACTERS HAS WON: `While all characters are important ... sequence comparisons using both pairwise sequence similarity and phylogenetic relationships have become one of the primary sets of characters used to define and distinguish virus taxa` | content_tags.findings[9] | 0.95 | the tagger's words |
| content_tags | DEFINITIONAL INHERITANCE IS STATED AS A RULE: `The properties that define higher-level taxa are shared with all lower-level taxa that belong to higher-level taxa` | content_tags.findings[10] | 0.95 | the tagger's words |
| content_tags | THREE PARALLEL BODIES, THREE CODES: the International Commission on Zoological Nomenclature for animals, the International Committee on Systematic Bacteriology for bacteria, the ICTV for viruses | content_tags.findings[11] | 0.95 | the tagger's words |
| content_tags | and the hierarchy is expected to move: `As new data are obtained ... the classification hierarchy may change` - a vocabulary that is correct AT A RELEASE NUMBER rather than simply correct | content_tags.findings[12] | 0.95 | the tagger's words |
| content_tags | and it is the only one of its kind: `No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy` | content_tags.findings[13] | 0.95 | the tagger's words |
| content_tags | `This process of classification and naming comprises the discipline of taxonomy`, dated to Linnaeus in the 18th century also in: taxonomy | content_tags.definitions[0] | 0.95 | the tagger's words |
| content_tags | the per-family criteria `used to define each new taxon`, `based upon the genetic and biological properties of the taxon members`, covering order, family, subfamily, genus and species also in: demarcation criteria | content_tags.definitions[1] | 0.95 | the tagger's words |
| content_tags | the database's enumerated fields - taxonomy level, `possible taxonomic changes from the previous release (new, split, move, merge, rename, and abolish)`, and genome type also in: controlled vocabulary | content_tags.definitions[2] | 0.95 | the tagger's words |
| content_tags | 6 — the enumerated change types - new, split, move, merge, rename, abolish | content_tags.quantities[0] | 0.95 | the tagger's words |
| content_tags | 42 — amino acid identity across the polyprotein, the demarcation criterion for the genus Enterovirus | content_tags.quantities[1] | 0.95 | the tagger's words |
| content_tags | 1966 — the committee's founding, as the International Committee on Nomenclature of Viruses; renamed in 1977 | content_tags.quantities[2] | 0.95 | the tagger's words |
| content_tags | the per-family criteria that decide whether a proposed taxon exists also in: demarcation criteria | content_tags.variables[0] | 0.95 | the tagger's words |
Tags that could not be placed in the text:
What was deliberately not tagged, and why, is recorded per paper by the tagger. Where a paper has no such record, this page says so rather than implying that nothing was declined.