phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| phenomenon | contamination that survives good laboratory practice and is invisible to the quality control usually used to detect it, biasing hardest exactly where biomass is lowest and the claims are most contested— “Contamination is often assumed to be absent if control samples do not yield a band on an agarose gel. However, band-less samples can generate non-negligible numbers of sequencing reads, suggesting that gel-based quality control is insufficient.” | |
| claim-type | method— “Decontam implements two simple de novo classification methods based on widely reproduced signatures of external contamination: (1) Sequences from contaminating taxa are likely to have frequencies that inversely correlate with sample DNA concentration and (2) sequences from contaminating taxa are likely to have higher prevalence in control… | |
| method — evidence | — “Let total sample DNA (T) be a mixture of two components (T = C + S): contaminating DNA (C) present in uniform concentration across samples and true sample DNA (S) present in varying concentration across samples.” | |
| object of study — evidence | — “However, the accuracy of marker-gene and metagenomic sequencing (MGS) is limited in practice by several processes that introduce contaminants—DNA sequences not truly present in the sampled community.” | |
| research question — evidence | — “Decontam implements two simple de novo classification methods based on widely reproduced signatures of external contamination: (1) Sequences from contaminating taxa are likely to have frequencies that inversely correlate with sample DNA concentration and (2) sequences from contaminating taxa are likely to have higher prevalence in control… | |
| contribution — evidence | — “Decontam implements two simple de novo classification methods based on widely reproduced signatures of external contamination: (1) Sequences from contaminating taxa are likely to have frequencies that inversely correlate with sample DNA concentration and (2) sequences from contaminating taxa are likely to have higher prevalence in control… | |
| transfer | from statistics: model comparison by ratio of sums-of-squared-residuals, carried from linear regression into a per-sequence classifier - and deliberately stripped of the inferential guarantee it carries in its home field— “The frequency-based score statistic is best thought of as a transformation that takes as input two values—the ratio of the sum-of-squared residuals, and the number of observations—and outputs a score that is a better classification statistic than the ratio of the sum-of-squared residuals alone.” | transfers[0] |
| transfer | from statistics: a two-component mixture model, carried from statistical modelling to represent total DNA as contaminant plus sample— “Let total sample DNA (T) be a mixture of two components (T = C + S): contaminating DNA (C) present in uniform concentration across samples and true sample DNA (S) present in varying concentration across samples.” | transfers[1] |
| mechanism | inverse frequency signature contaminant DNA enters at roughly constant absolute concentration while sample DNA varies, so as a proportion of the total the contaminant's frequency falls as sample concentration rises - a slope of -1 in log space against a slope of 0— “Let total sample DNA (T) be a mixture of two components (T = C + S): contaminating DNA (C) present in uniform concentration across samples and true sample DNA (S) present in varying concentration across samples.” | mechanisms[0] |
| mechanism | prevalence signature in negative controls with no competing sample DNA, a negative control's sequencing capacity is available to whatever contaminant is present, so contaminants are detected in a larger fraction of controls than of true samples— “Decontam implements two simple de novo classification methods based on widely reproduced signatures of external contamination: (1) Sequences from contaminating taxa are likely to have frequencies that inversely correlate with sample DNA concentration and (2) sequences from contaminating taxa are likely to have higher prevalence in control… | mechanisms[1] |
| mechanism | biomass-correlated confounding because the frequency method reads low sample concentration as evidence of contamination, any real sequence that is genuinely commoner in low-biomass samples presents with the contaminant signature - so mixing environments manufactures false positives out of true biology— “The assumptions of decontam, especially the frequency method, can be violated if bacterial biomass systematically differs between groups of samples. For example, if decontam were applied to a mixed set of stool (high biomass) and airway (low biomass) samples, real sequences in the airway samples could be classified as contaminants, because… | mechanisms[2] |
| critiques | gel-band quality control as evidence that a sequencing run is free of contamination— “Contamination is often assumed to be absent if control samples do not yield a band on an agarose gel. However, band-less samples can generate non-negligible numbers of sequencing reads, suggesting that gel-based quality control is insufficient.” | claim_relations[0] |
| critiques | ad hoc in silico decontamination - abundance thresholds, negative-control subtraction and contaminant blacklists— “However, relative abundance thresholds remove rare features truly present in the sample and do not remove abundant contaminants that are the most likely to interfere with subsequent analysis.” | claim_relations[1] |
| builds-on | prior reports of the two contaminant signatures: inverse correlation with DNA concentration, and presence in negative controls— “Decontam implements two simple de novo classification methods based on widely reproduced signatures of external contamination: (1) Sequences from contaminating taxa are likely to have frequencies that inversely correlate with sample DNA concentration and (2) sequences from contaminating taxa are likely to have higher prevalence in control… | claim_relations[2] |
| confirms | the conclusion that marker-gene data from placenta biopsies do not support an indigenous placenta microbiome— “The application of decontam to 16S rRNA gene sequencing data generated from placenta biopsies corroborated the conclusion that the data did not support the existence of a placenta microbiome.” | claim_relations[3] |
| sense | score statistic P - AS COMPUTED: set equal to a p-value from the chi-square or Fisher's exact test, and so arithmetically indistinguishable from one— “Although the prevalence-based score statistic is set equal to a p-value from the chi-square or Fisher’s exact tests, it is used by decontam only as a score that effectively distinguishes between the contaminant and non-contaminant mixture components.” | senses[0] |
| sense | score statistic P - AS LICENSED: a classification score only, explicitly carrying no guarantee on the type 1 error rate. The paper states the difference rather than leaving it to the reader— “Although inspired by the general linear F test, the frequency-based score statistic is not a p value, i.e., it is not associated with any guarantees on the type 1 error rate.” | senses[1] |
| sense | accuracy of decontam - PER SEQUENCE FEATURE: specificity and sensitivity described as sometimes moderate— “The sensitivity of contaminant identification increased substantially with feature prevalence. As a result, while the specificity and sensitivity of decontam on a per-feature basis were sometimes… | senses[2] |
| sense | accuracy of decontam - PER READ: described as reaching exceptional levels, on the same classifications of the same data. The unit of account decides which number is reported | senses[3] |
| control | the field's standard check that a negative control shows no band on an agarose gel, taken as evidence that contamination is absent — absent-stated-about-other Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out contamination in the sequencing library - and the paper's own sentence says this check does NOT eliminate it, because band-less samples still generate non-negligible reads Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[0] |
| control | removing every sequence that appears in a negative control — absent-stated-about-other Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out contaminant sequences - and it OVER-removes, because cross-contamination puts abundant TRUE sequences into the negative controls Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[1] |
| control | discarding sequences below an ad hoc relative abundance threshold — absent-stated-about-other Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out abundant contaminants, which it fails to remove, while removing rare features that are truly present in the sample Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[2] |
| control | excluding taxa on a blacklist of previously reported contaminants — absent-stated-about-other Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out previously reported contaminants - leaving study-specific contaminants in place and removing true sequences Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[3] |
| control | cross-checking taxonomic assignments against a second controlled vocabulary, HOMD against SILVA, at the genus level — partial Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out a contaminant call that is an artefact of one reference vocabulary's genus boundaries Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[4] |
| control | an explicit 'ambiguous' class for genera that neither reference database resolves, instead of forcing every genus into contaminant or oral — held Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out a genus with no evidence either way being forced into 'contaminant' or 'oral' and counted as if it had been decided Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[5] |
| control | turning the method on a published low-biomass claim - the placenta microbiome - where the expected answer was already contested — held Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out a decontamination method validated only on data where the right answer was chosen by the people validating it Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[6] |
| weight | gel-band quality control as evidence that a sequencing run is free of contamination — 0.9 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[0] |
| weight | ad hoc in silico decontamination - abundance thresholds, negative-control subtraction and contaminant blacklists — 0.9 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[1] |
| weight | prior reports of the two contaminant signatures: inverse correlation with DNA concentration, and presence in negative controls — 0.9 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[2] |
| weight | the conclusion that marker-gene data from placenta biopsies do not support an indigenous placenta microbiome — 0.85 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[3] |
| differs in (stated by the tagger, no quotation) | score statistic —distinct-from→ p value — whether it licenses a claim about the type 1 error rate | concept_edges[0] |
| relation | score statistic —distinct-from→ p value — computed the same way and carrying none of the same guarantees Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[0] |
| weight | score statistic —distinct-from→ p value — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[0] |
| differs in (stated by the tagger, no quotation) | contaminants —distinct-from→ true community members — whether the sequence originated in the sampled environment | concept_edges[1] |
| relation | contaminants —distinct-from→ true community members — assumed to be disjoint populations - the assumption the whole method rests on Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[1] |
| weight | contaminants —distinct-from→ true community members — 0.9 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[1] |
| differs in (stated by the tagger, no quotation) | cross-contamination —distinct-from→ External contamination — whether the contaminating DNA came from outside the study or from another sample in it | concept_edges[2] |
| relation | cross-contamination —distinct-from→ External contamination — different sources, and different statistical signatures in the data Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[2] |
| weight | cross-contamination —distinct-from→ External contamination — 0.9 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[2] |
| outcome | control — absent-stated-about-other Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[0] |
| outcome | control — absent-stated-about-other Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[1] |
| outcome | control — absent-stated-about-other Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[2] |
| outcome | control — absent-stated-about-other Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[3] |
| outcome | control — partial Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[4] |
| outcome | control — held Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[5] |
| outcome | control — held Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[6] |
| limitation | decontam is not designed for cross-contamination, which violates its founding assumption that contaminants and true members are distinct populations Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[0] |
| limitation | the frequency method's approximations break down in exactly the low-biomass regime where contamination matters most - when contaminants are a large fraction of reads Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[1] |
| limitation | applying it across environments of systematically different biomass can classify real sequences as contaminants, because low concentration is the contaminant signature Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[2] |
| limitation | it depends on patterns across samples, so it has low sensitivity for contaminants present in very few samples - the tail it cannot see Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[3] |
| limitation | the default classification threshold is not recommended as-is: the authors direct users to read a threshold off their own score histogram instead Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[4] |
| limitation | the method is less effective when groups of samples carry systematically different contaminant patterns, which is why batches must be declared by the user rather than detected Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[5] |
finding · quantity · variable · definition · key-term — grounded in the full text| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[0] |
| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[1] |
| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[2] |
| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[3] |
| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[4] |
| quantity | the default classification threshold, which the authors recommend against using unexamined Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[0] |
| quantity | the threshold at which classification reduces to 'is the contaminant model the better fit' Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[1] |
| quantity | sequences on which the two reference databases disagreed, resolved by BLAST Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[2] |
| variable | sample DNA concentration Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[0] |
| variable | prevalence Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[1] |
| definition | contaminants Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[0] |
| definition | External contamination Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[1] |
| definition | score statistic Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[2] |
| concept | contaminants — not defined in this paper's own words; DNA sequences not truly present in the sampled community - defined by provenance rather than by anything observable in the sequence itself Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[0] |
| concept | External contamination — not defined in this paper's own words; contributed from outside the samples being measured - reagents, instruments, surfaces, bodies. The type decontam is built for Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[1] |
| concept | cross-contamination — not defined in this paper's own words; samples mixing with each other during processing or sequencing - the type decontam explicitly does not address, because its statistical signature is different Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[2] |
| concept | score statistic — not defined in this paper's own words; a number computed as a tail probability and licensed only as a classification score - the paper's own distinction, stated twice Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[3] |
| concept | p value — not defined in this paper's own words; the reading the score statistic invites and the paper refuses: it carries no type 1 error guarantee Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[4] |
| concept | classification threshold — not defined in this paper's own words; P*, compared against the score to classify; default 0.1, and the authors tell users not to trust the default without inspecting their own score distribution Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[5] |
| concept | negative controls — not defined in this paper's own words; reagent-only or blank samples processed alongside real ones - the input to the prevalence method, and the thing whose gel band was wrongly treated as the test Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[6] |
| concept | gel-based quality control — not defined in this paper's own words; checking whether a control sample yields a band on an agarose gel - argued here to be insufficient, because band-less samples still generate reads Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[7] |
| concept | relative abundance thresholds — not defined in this paper's own words; the commonest in silico decontamination practice, which removes rare true sequences and keeps abundant contaminants - wrong at both ends Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[8] |
| concept | true community members — not defined in this paper's own words; the sequences actually present in the sampled environment, assumed distinct from contaminants - an assumption cross-contamination violates Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[9] |
| concept | low-biomass — not defined in this paper's own words; the regime where contaminant DNA approaches or exceeds sample DNA, breaking the frequency method's approximations and producing the field's most contested claims Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[10] |
| concept | SILVA — not defined in this paper's own words; one of two taxonomic references used to name the sequences, and one half of a disagreement resolved by a third method Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[11] |
| concept | HOMD — not defined in this paper's own words; the Human Oral Microbiome Database, the other half of that disagreement Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[12] |
| concept | processing batches — not defined in this paper's own words; user-declared groups scored independently, because separately processed samples can carry different contaminants Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[13] |
| concept | placenta microbiome — not defined in this paper's own words; a contested claim the method was turned on: applying decontam corroborated that the data do not support it Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[14] |
| general linear F test | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[0] |
| type 1 error rate | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[1] |
| chi-square | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[2] |
| Fisher’s exact tests | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[3] |
| specificity | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[4] |
| sensitivity | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.statistics[5] |
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.
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