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 WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below.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 An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason.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.| 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 |
| transfer | transfers | a method or concept carried in from another field |
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; 3 of 3 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 | contaminant DNA in marker-gene and metagenomic sequencing - sequences that are in the data and not in the sample - and how to identify them without knowing in advance what they are Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | object_of_study | the paper's words | |
| research_question | whether contaminant sequences can be separated from true community members de novo, using only statistical patterns already present in a standard sequencing run Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | research_question | the paper's words | |
| contribution | decontam: two independent classifiers built on two reproduced signatures of contamination - inverse correlation with DNA concentration, and higher prevalence in negative controls - released as an R package Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | contribution | the paper's words | |
| claim_type | method Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_type | the paper's words | |
| 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | phenomenon | the paper's words | |
| method | system-or-tool-building Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: system-or-tool-building | method | the paper's words | |
| mechanisms | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: inverse frequency signature | mechanisms[0] | 0.95 | the tagger's words |
| mechanisms | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[1] | 0.95 | the tagger's words |
| mechanisms | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: biomass-correlated confounding | mechanisms[2] | 0.95 | the tagger's words |
| limitations | decontam is not designed for cross-contamination, which violates its founding assumption that contaminants and true members are distinct populations Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[0] | 0.95 | the tagger's words |
| limitations | 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 record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[1] | 0.95 | the tagger's words |
| limitations | applying it across environments of systematically different biomass can classify real sequences as contaminants, because low concentration is the contaminant signature Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[2] | 0.95 | the tagger's words |
| limitations | 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 record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[3] | 0.95 | the tagger's words |
| limitations | 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 record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[4] | 0.95 | the tagger's words |
| limitations | 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 record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[5] | 0.95 | the tagger's words |
| transfers | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | transfers[0] | 0.95 | the tagger's words |
| transfers | a two-component mixture model, carried from statistical modelling to represent total DNA as contaminant plus sample Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | transfers[1] | 0.95 | the tagger's words |
| controls | the field's standard check that a negative control shows no band on an agarose gel, taken as evidence that contamination is absent Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: 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 · outcome: absent-stated-about-other | controls[0] | 0.95 | the tagger's words |
| controls | removing every sequence that appears in a negative control Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: contaminant sequences - and it OVER-removes, because cross-contamination puts abundant TRUE sequences into the negative controls · outcome: absent-stated-about-other | controls[1] | 0.95 | the tagger's words |
| controls | discarding sequences below an ad hoc relative abundance threshold Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: abundant contaminants, which it fails to remove, while removing rare features that are truly present in the sample · outcome: absent-stated-about-other | controls[2] | 0.95 | the tagger's words |
| controls | excluding taxa on a blacklist of previously reported contaminants Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: previously reported contaminants - leaving study-specific contaminants in place and removing true sequences · outcome: absent-stated-about-other | controls[3] | 0.95 | the tagger's words |
| controls | cross-checking taxonomic assignments against a second controlled vocabulary, HOMD against SILVA, at the genus level Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a contaminant call that is an artefact of one reference vocabulary's genus boundaries · outcome: partial | controls[4] | 0.95 | the tagger's words |
| controls | an explicit 'ambiguous' class for genera that neither reference database resolves, instead of forcing every genus into contaminant or oral Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a genus with no evidence either way being forced into 'contaminant' or 'oral' and counted as if it had been decided · outcome: held | controls[5] | 0.95 | the tagger's words |
| controls | turning the method on a published low-biomass claim - the placenta microbiome - where the expected answer was already contested Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a decontamination method validated only on data where the right answer was chosen by the people validating it · outcome: held | controls[6] | 0.95 | the tagger's words |
| concepts | contaminants Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: contaminants | concepts[0] | 0.95 | the paper's words |
| concepts | External contamination Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: External contamination | concepts[1] | 0.95 | the paper's words |
| concepts | cross-contamination Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: cross-contamination | concepts[2] | 0.95 | the paper's words |
| concepts | score statistic Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: score statistic | concepts[3] | 0.95 | the paper's words |
| concepts | p value Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: p value | concepts[4] | 0.95 | the paper's words |
| concepts | classification threshold Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: classification threshold | concepts[5] | 0.95 | the paper's words |
| concepts | negative controls Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: negative controls | concepts[6] | 0.95 | the paper's words |
| concepts | gel-based quality control Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: gel-based quality control | concepts[7] | 0.95 | the paper's words |
| concepts | relative abundance thresholds Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: relative abundance thresholds | concepts[8] | 0.95 | the paper's words |
| concepts | true community members Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: true community members | concepts[9] | 0.95 | the paper's words |
| concepts | low-biomass Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: low-biomass | concepts[10] | 0.95 | the paper's words |
| concepts | SILVA Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: SILVA | concepts[11] | 0.95 | the paper's words |
| concepts | HOMD Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: HOMD | concepts[12] | 0.95 | the paper's words |
| concepts | processing batches Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: processing batches | concepts[13] | 0.95 | the paper's words |
| concepts | placenta microbiome Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: placenta microbiome | concepts[14] | 0.95 | the paper's words |
| senses | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[0] | 0.95 | the tagger's words |
| senses | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[1] | 0.95 | the tagger's words |
| senses | accuracy of decontam - PER SEQUENCE FEATURE: specificity and sensitivity described as sometimes moderate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[2] | 0.95 | the tagger's words |
| senses | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[3] | 0.95 | the tagger's words |
| claim_relations | critiques → gel-band quality control as evidence that a sequencing run is free of contamination Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[0] | 0.95 | the tagger's words |
| claim_relations | critiques → ad hoc in silico decontamination - abundance thresholds, negative-control subtraction and contaminant blacklists Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[1] | 0.95 | the tagger's words |
| claim_relations | builds-on → prior reports of the two contaminant signatures: inverse correlation with DNA concentration, and presence in negative controls Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[2] | 0.95 | the tagger's words |
| claim_relations | confirms → the conclusion that marker-gene data from placenta biopsies do not support an indigenous placenta microbiome Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[3] | 0.95 | the tagger's words |
| concept_edges | score statistic —distinct-from→ p value Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: whether it licenses a claim about the type 1 error rate · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): whether it licenses a claim about the type 1 error rate · the relation stated: computed the same way and carrying none of the same guarantees also in: score statistic · p value | concept_edges[0] | 0.95 | the tagger's words |
| concept_edges | contaminants —distinct-from→ true community members Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: whether the sequence originated in the sampled environment · the relation itself is separately evidenced · strength of the relation: 0.9 · differs in (stated by the tagger, no quotation): whether the sequence originated in the sampled environment · the relation stated: assumed to be disjoint populations - the assumption the whole method rests on also in: contaminants · true community members | concept_edges[1] | 0.95 | the tagger's words |
| concept_edges | cross-contamination —distinct-from→ External contamination Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: whether the contaminating DNA came from outside the study or from another sample in it · the relation itself is separately evidenced · strength of the relation: 0.9 · differs in (stated by the tagger, no quotation): whether the contaminating DNA came from outside the study or from another sample in it · the relation stated: different sources, and different statistical signatures in the data also in: cross-contamination · External contamination | concept_edges[2] | 0.95 | the tagger's words |
| content_tags | the score decontam reports is computed as a tail probability and is explicitly not a p value - it carries no type 1 error guarantee Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[0] | 0.95 | the tagger's words |
| content_tags | the same classifications are 'sometimes moderate' per sequence feature and 'exceptional' per read - the unit of account decides the number Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[1] | 0.95 | the tagger's words |
| content_tags | the field's usual contamination control - no band on a gel - does not work, because band-less samples still generate substantial reads Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[2] | 0.95 | the tagger's words |
| content_tags | two curated taxonomic databases disagreed on 80 sequences and the disagreement had to be settled by a third method Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[3] | 0.95 | the tagger's words |
| content_tags | Frequency-based contaminant identification is not recommended for extremely low-biomass samples, where its approximations break down. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[4] | 0.95 | the tagger's words |
| content_tags | DNA sequences not truly present in the sampled community - a definition by provenance, so nothing in the sequence itself can settle it Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: contaminants | content_tags.definitions[0] | 0.95 | the tagger's words |
| content_tags | contributed from outside the samples being measured; distinguished from internal or cross-contamination, which arises when samples mix with each other Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: External contamination | content_tags.definitions[1] | 0.95 | the tagger's words |
| content_tags | a transformation taking the ratio of sums-of-squared residuals and the number of observations, and returning a better classification statistic than the ratio alone - explicitly not a p value Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: score statistic | content_tags.definitions[2] | 0.95 | the tagger's words |
| content_tags | the default classification threshold, which the authors recommend against using unexamined Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[0] | 0.95 | the tagger's words |
| content_tags | the threshold at which classification reduces to 'is the contaminant model the better fit' Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[1] | 0.95 | the tagger's words |
| content_tags | sequences on which the two reference databases disagreed, resolved by BLAST Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[2] | 0.85 | the tagger's words |
| content_tags | general linear F test Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: general linear F test | content_tags.statistics[0] | 0.95 | the tagger's words |
| content_tags | type 1 error rate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: type 1 error rate | content_tags.statistics[1] | 0.95 | the tagger's words |
| content_tags | chi-square Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: chi-square | content_tags.statistics[2] | 0.95 | the tagger's words |
| content_tags | Fisher’s exact tests Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Fisher’s exact tests | content_tags.statistics[3] | 0.95 | the tagger's words |
| content_tags | specificity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: specificity | content_tags.statistics[4] | 0.95 | the tagger's words |
| content_tags | sensitivity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: sensitivity | content_tags.statistics[5] | 0.95 | the tagger's words |
| content_tags | sample DNA concentration Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: sample DNA concentration | content_tags.variables[0] | 0.95 | the tagger's words |
| content_tags | prevalence Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: prevalence | content_tags.variables[1] | 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.