UniProt: a worldwide hub of protein knowledge

The UniProt Consortium · Nucleic Acids Research · 2018 · genetics · 10.1093/nar/gky1049 · record dogan2018-uniprot-a-worldwide-hub-of-protein
tag layer · index · concepts · authors · עברית
Where this record's text came from. 2026-08-20 schema-0.3 pass: every quote verified as an exact substring of the staged text and anchored at merge time; concept terms verified present; every edge endpoint an existing node.
How to read this page. The article itself is not reproduced here — this paper is not cleared for redistribution, so what follows is the tag layer alone. The evidence sentences are withheld with the article. The table at the foot lists every tag the record carries; each row names the facet it belongs to, and the whose words column says whether the tag records the paper's own wording or the tagger's sentence about the paper. Every tag links to each other paper in the corpus carrying it. The machine-readable edition of the same thing is the TEI file beside this one, where the tags live in standOff, and the article is at its publisher via the link below. 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 WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below.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 An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason.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 for that row; on this page it is withheld with the article, and the article is at its publisher. 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.

Tags on this paper

Every tag the record carries, each linking to every other paper in the corpus that carries it. A tag appears here whether or not its words occur in the article — the spans below are only the ones a sentence in this paper licenses. Of the 15 concept tags on this paper, all 15 are grounded in a quoted sentence.
UniProtKB annotations evidences expert biocuration CAUTION UniParc redundancy removal InterPro GO annotation UPCLASS UniFire curatable literature METTL14 METTL3 MAGs annotation propagation redundancy from near-identical strains domain architecture conservative propagation UniProt Knowledgebase CAUTION comment UniProt Archive rule-based prediction systems system-or-tool-building
Method, as described: expert biocuration into Swiss-Prot, rule-based automatic annotation into TrEMBL, redundancy removal into an archive rather than deletion, and evidence tags on every claim from either route

Legend

relation to other workclaim_relationshow this paper stands to another: agrees, contradicts, extends, qualifies
claim typeclaim_typethe shape of the claim: existence, mechanism, method, critique, prediction, null
concept edgeconcept_edgesan asserted relation between two concepts, with the sentence asserting it
conceptconceptsan idea the paper works with, quoted where the paper uses it
content tagcontent_tagsa finding, definition, quantity, statistic or variable named in the paper
contributioncontributionwhat the paper claims to add
controlcontrolsan experiment run to eliminate a rival explanation
limitationlimitationswhat the paper says its evidence cannot support
mechanismmechanismshow the reported effect is said to come about
methodmethodhow the paper produced its evidence
object of studyobject_of_studywhat the paper is about — the thing it investigates
phenomenonphenomenonthe effect or regularity under study
research questionresearch_questionthe question the paper sets itself
sensesensesa distinct use of a term, quoted where the paper fixes it
unrecordable relationunhoused_relationsa relation the paper asserts that this vocabulary cannot express, with the reason

The paper

The full text is not reproduced here. This article is not cleared for redistribution, so the page carries the tag layer only. Its evidence sentences are withheld; the grounding status remains with each tag, and the article itself is at https://doi.org/10.1093/nar/gky1049. The reading view exists for the papers whose licence permits it.

Every tag on this page

claim_relations 5 · claim_type 1 · concept_edges 5 · concepts 15 · content_tags 15 · contribution 1 · controls 8 · limitations 7 · mechanisms 4 · method 1 · object_of_study 1 · phenomenon 1 · research_question 1 · senses 6 · unhoused_relations 2

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 5 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.

facettagfieldconf.whose words
object_of_studythe UniProt Knowledgebase itself - 120 million protein records, of which just over half a million carry annotations a human curator read out of the literature
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
object_of_studythe paper's words
research_questionhow to keep a knowledge base current, provenance-tracked and correct while the sequence data entering it grows exponentially
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
research_questionthe paper's words
contributiona two-year update: expanded reference proteomes especially for viruses, new rule-based and association-rule annotation systems, a bibliography layer built from other databases and text mining, and a licence change to CC-BY 4.0
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
contributionthe paper's words
claim_typemethod
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
claim_typethe paper's words
phenomenonthe gap between what has been sequenced and what has been read - 120 million entries against half a million with curated annotation, and expert curation reaching 35-50% of the curatable literature
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
phenomenonthe paper's words
methodsystem-or-tool-building
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
methodthe paper's words
mechanismswhy one wrong curated record matters far beyond itself: functional data is computationally transferred from Swiss-Prot to sequence-related but less studied proteins in TrEMBL, so a correction upstream stops misleading data being added to orthologues on the strength of an over-predictive signature
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[0]0.95the tagger's words
mechanismsthe growth problem is not more biology but more of the same: 90% of proteins have over 90% identity because sequencing is driven by very similar strains of the same species
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[1]0.95the tagger's words
mechanismsthe premise of the DAAC predictor - that function depends not only on WHICH domains a protein has but on their arrangement and order, so two proteins with the same domain set can do different things
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[2]0.85the tagger's words
mechanismshow a cluster-level GO term is earned: it is assigned only when every annotated member carries it, or when it is a common ancestor of at least one term from each - agreement across the cluster rather than a majority
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
mechanisms[3]0.95the tagger's words
limitationsexpert biocuration reaches only 35-45% of the curatable literature for a species, 50% for humans - the coverage gap is measured and published rather than left implicit
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[0]0.95the tagger's words
limitationscuration is labour intensive and the authors defend it anyway as the most efficient way to get everything out of a paper - which is a statement about what automation has NOT replaced
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[1]0.95the tagger's words
limitationskeeping a record current is hard because knowledge of protein function evolves and new techniques produce results that may appear to contradict earlier observations
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[2]0.95the tagger's words
limitationsMECHANISMS TO IDENTIFY AND HIGHLIGHT CONTRADICTORY INFORMATION IN EXISTING ENTRIES ARE A FUTURE PLAN, NOT A CAPABILITY - a 120-million-record knowledge base with per-claim evidence still cannot systematically surface where its own entries disagree
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[3]0.95the tagger's words
limitationsredundancy removal is not applied to viruses at all, because their small genomes carry too many variants - a stated exemption with a stated reason
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[4]0.95the tagger's words
limitationsUPCLASS, the classifier applied to 32 million accession-PMID pairs, has a published recall of 0.62 - so roughly a third of the classifications it should make, it does not
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[5]0.95the tagger's words
limitationsthe categorisation of computationally mapped bibliography by source database is described by the authors as not optimal for all literature, which is why the classifier was brought in
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
limitations[6]0.85the tagger's words
controlsan evidence tag on every individual piece of captured knowledge, naming its source
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: a claim in the database being untraceable to where it came from - and it is not restricted to the curated half: automatic annotations carry which system produced them · outcome: held
controls[0]0.95the tagger's words
controlsa CAUTION comment recording that a previously reported activity is an unsafe observation, kept on the entry alongside the annotation
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: a superseded finding either persisting silently or disappearing without trace - the reader gets the claim, the doubt and the reason together · outcome: held
controls[1]0.95the tagger's words
controlsredundancy removal that moves ~38% of complete proteomes out of UniProtKB and into UniParc, which retains historical obsolete sequence
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: growth in near-identical strains swamping the knowledgebase - WITHOUT losing the sequences, which is the difference between a withdrawal and a deletion · outcome: held
controls[2]0.95the tagger's words
controlsassigning a GO term to a UniRef cluster only when EVERY annotated member has it, or when it is a common ancestor of at least one term from each
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: a single member's annotation propagating to a whole cluster - the rule requires unanimity or a shared ancestor, not a majority · outcome: held
controls[3]0.95the tagger's words
controlspublishing UPCLASS's precision, recall and F-score before applying it at scale
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: the classifier's error rate being invisible to users of the 32 million pairs it classified - PARTIAL, because knowing recall is 0.62 does not tell a user WHICH third is missing · outcome: partial
controls[4]0.95the tagger's words
controlsprioritising for curation exactly what computational prediction gets WRONG - proteins a signature would place in an enzyme family but which are non-functional through the loss of specific residues
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: human effort being spent where the automatic systems already succeed, and leaves the curators on the cases where a prediction would be confidently wrong · outcome: held
controls[5]0.95the tagger's words
controlsadmitting metagenome-assembled genomes only when they show high completeness and low contamination, and removing segmented viruses missing one or more segments
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: partial or contaminated assemblies entering the knowledgebase as if they were whole proteomes · outcome: held
controls[6]0.95the tagger's words
controlsre-importing curated data from the domain-specific resources it was contributed to - IMEx, the Complex Portal, GO - rather than duplicating their maintenance
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
eliminates: the same fact diverging between UniProt and the specialist database that owns it; each is stored and maintained where it belongs and flows back · outcome: held
controls[7]0.9the tagger's words
conceptsUniProtKB
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: UniProtKB
concepts[0]0.95the paper's words
conceptsannotations
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: annotations
concepts[1]0.95the paper's words
conceptsevidences
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: evidences
concepts[2]0.95the paper's words
conceptsexpert biocuration
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
concepts[3]0.95the paper's words
conceptsCAUTION
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: CAUTION
concepts[4]0.95the paper's words
conceptsUniParc
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: UniParc
concepts[5]0.95the paper's words
conceptsredundancy removal
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
concepts[6]0.95the paper's words
conceptsInterPro
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: InterPro
concepts[7]0.95the paper's words
conceptsGO annotation
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: GO annotation
concepts[8]0.95the paper's words
conceptsUPCLASS
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: UPCLASS
concepts[9]0.95the paper's words
conceptsUniFire
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: UniFire
concepts[10]0.95the paper's words
conceptscuratable literature
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
concepts[11]0.95the paper's words
conceptsMETTL14
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: METTL14
concepts[12]0.95the paper's words
conceptsMETTL3
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: METTL3
concepts[13]0.95the paper's words
conceptsMAGs
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: MAGs
concepts[14]0.95the paper's words
unhoused_relationsCAUTION → METTL14
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
A RECORD HOLDING A CLAIM AND A DOUBT ABOUT THAT CLAIM AT ONCE. The entry keeps the reported methyltransferase activity AND a comment saying the report is an unsafe observation. There is no edge type for 'this annotation is flagged as unreliable' - all eight assert that a relation holds, and the whole content of a CAUTION is that something asserted elsewhere should not be relied on. This is the project's quine1951 finding with a WORKING IMPLEMENTATION on the other side: UniProt can write it and we cannot
unhoused_relations[0]the tagger's words
unhoused_relationsexpert biocuration → curatable literature
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
A COVERAGE RATIO, WHICH IS A RELATION BETWEEN AN ACTIVITY AND WHAT IT HAS NOT REACHED. Curation captures 35-45% of the curatable literature per species, 50% for humans. 'part-of' is wrong, 'causes' is wrong, and there is no type for 'X covers this fraction of Y' - which is the single most useful thing a knowledge base can say about itself and the thing our own corpus has never stated about its own coverage
unhoused_relations[1]the tagger's words
sensesreviewed versus unreviewed - NOT A QUALITY GRADE BUT A PROVENANCE CLASS, and the two are wildly different sizes. `Reviewed` means a curator assimilated multiple lines of evidence from a paper's text and figures; `unreviewed` means a rule fired. Half a million against 120 million. A user filtering to `reviewed` is not filtering out errors, they are filtering to the fraction a person has read
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
senses[0]0.95the tagger's words
sensesevidence, in UniProt - A SOURCE TAG ON EVERY INDIVIDUAL CLAIM, not a citation on the record. Each piece of knowledge carries where it came from, and automatic annotations carry which system produced them. This is the same commitment this corpus makes with its `evidence` field, made by a database three orders of magnitude larger
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
senses[1]0.95the tagger's words
sensesCAUTION - A COMMENT TYPE THAT SAYS A PUBLISHED FINDING IS UNSAFE. When structural work showed METTL14 has a degenerate active site, the earlier reported methyltransferase activity was not deleted and not silently overwritten: a CAUTION comment was added to tell users the initial report is `an unsafe observation`. THE RECORD CARRIES BOTH THE CLAIM AND THE DOUBT
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
senses[2]0.95the tagger's words
sensesremoved, of a proteome - MOVED TO AN ARCHIVE, NOT DELETED. Redundancy removal has taken about 38% of complete proteomes out of UniProtKB and placed their sequences in UniParc, which holds a complete set of known sequences including historical obsolete ones. A withdrawal convention at the scale of 241 million proteins
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
senses[3]0.95the tagger's words
sensesprediction precision, of the UniRef GO propagation - MEASURED AGAINST ITS OWN EARLIER OUTPUT. The >97% figure comes from comparing sequences that newly acquired a GO annotation with ones the same system annotated in previous releases. That is self-consistency across releases, which is worth knowing and is not external validation against experiment
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
senses[4]0.9the tagger's words
sensescuratable literature - THE DENOMINATOR THEY MEASURE THEMSELVES AGAINST, and it is not the literature. Coverage of 35-45%, rising to 50% for humans, is a share of the papers judged curatable for a species, so a paper outside that judgement is not counted as missed
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
senses[5]0.9the tagger's words
claim_relationscontradicts → the initial characterisation of METTL14 as a methyltransferase, based on reported activity and MT-A70 family membership
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
note: 'contradicts' is right here and it was not for cruz-jentoft2018's mass criterion. The paper does not demote the earlier claim, it reports that structural work showed the active site is degenerate and cannot accommodate the substrates - the earlier finding is not narrowed, it is wrong, and UniProt flags it as unsafe rather than deleting it
claim_relations[0]0.95the tagger's words
claim_relationsextends → the UniProt Consortium's own previous database update, published in the same journal in 2017
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
claim_relations[1]0.9the tagger's words
claim_relationsbuilds-on → InterPro and its member databases PROSITE, SMART and Pfam, whose predictive signatures classify sequences and predict domains for the unreviewed records
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
claim_relations[2]0.95the tagger's words
claim_relationspredicts → the authors of future papers, who are asked to write protein mentions as (UniProtKB: P68369) so curators and text-mining tools can connect their work
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
note: an instruction to a literature that does not exist yet, and the paper defers to any journal that already has its own format - a standard proposed with its own exception attached
claim_relations[3]0.9the tagger's words
claim_relationsbuilds-on → the specialist resources this data is contributed to and re-imported from - the IMEx Consortium, the Complex Portal and the Gene Ontology
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
claim_relations[4]0.95the tagger's words
concept_edgesannotations —part-of→ UniProtKB
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
strength of the relation: 1
concept_edges[0]the tagger's words
concept_edgesevidences —part-of→ annotations
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
strength of the relation: 0.95 · note: RETYPED IN THE AUDIT from 'annotations --operationalised-as--> evidences', where my own note conceded it was not a measurement relation. The quote says every piece of knowledge is ASSOCIATED WITH evidences, which is attachment - and attachment is what 'part-of' says Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span writes 'every piece of knowledge we capture is associated with evidences', not 'annotations'.
concept_edges[1]the tagger's words
concept_edgesCAUTION —part-of→ annotations
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
strength of the relation: 0.9 · note: a comment type carried on an entry beside its annotation - the mechanism by which a record holds a claim and a doubt about that claim at the same time Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span writes 'a CAUTION comment to the METTL14 entry', not 'annotations'.
also in: CAUTION · annotations
concept_edges[2]the tagger's words
concept_edgesMETTL3 —distinct-from→ METTL14
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
strength of the relation: 1 · note: and the distinction is the whole point: they are both MT-A70 family members and both were reported to have methyltransferase activity. Only one has a working active site
also in: METTL3 · METTL14
concept_edges[3]the tagger's words
concept_edgesredundancy removal —causes→ UniProtKB
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
direction on the measure: reduces · strength of the relation: 0.9 · note: and the reduction is the point - the paper reports that it made growth scalable rather than merely smaller Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but endpoint by anaphora: 'this process' = the redundancy removal process (previous sentences).
concept_edges[4]the tagger's words
content_tags120 million protein entries, of which just over half a million carry annotations extracted from the literature by expert curators
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[0]0.95the tagger's words
content_tagsexpert biocuration reaches 35-45% of the curatable literature per species, 50% for humans
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[1]0.95the tagger's words
content_tagsRedundancy removal has taken about 38% of all complete proteomes (about 241 million proteins) out of UniProtKB.
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[2]0.95the tagger's words
content_tagsVirus reference proteomes stood at 428 at the previous publication, about an order of magnitude below the 4405 known viral species.
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[3]0.95the tagger's words
content_tagsStructural studies showed only METTL3 is catalytic; METTL14 has a degenerate active site and a non-catalytic role.
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[4]0.95the tagger's words
content_tagsthe bibliography layer adds 902,956 unique papers over 363,591 entries, and 36,147,401 accession-PMID pairs
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[5]0.95the tagger's words
content_tagsUniProt data moved to a CC-BY 4.0 licence to make reuse easier - stated in the paper itself
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.findings[6]0.95the tagger's words
content_tagsUniProtKB = reviewed Swiss-Prot entries curated by an expert team, plus unreviewed TrEMBL entries annotated by automated and rule-based systems
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.definitions[0]0.95the tagger's words
content_tagsevidences = the source tag attached to every individual piece of captured knowledge
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
also in: evidences
content_tags.definitions[1]0.95the tagger's words
content_tagsCAUTION = a comment telling users that an initially reported finding is an unsafe observation
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.definitions[2]0.95the tagger's words
content_tagsUniParc = the archive holding a complete set of known sequences including historical obsolete ones, where redundancy-removed proteomes go
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.definitions[3]0.95the tagger's words
content_tagsUPCLASS precision 0.80, recall 0.62, F-score 0.70 - published before being applied to 32 million accession-PMID pairs
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.statistics[0]0.95the tagger's words
content_tagsUniRef GO propagation precision above 97% in all three GO domains - measured by comparing newly annotated sequences against the system's own earlier releases
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.statistics[1]0.95the tagger's words
content_tags90% of proteins have over 90% identity to another, which is what makes the growth a redundancy problem rather than a knowledge one
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.statistics[2]0.95the tagger's words
content_tagsthe two rule systems: UniRule and the Statistical Automatic Annotation System
Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above.
content_tags.variables[1]0.95the tagger's words

Interpretive choices

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.

© 2026 Shir Sivroni · ORCID 0009-0000-2597-2824