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 WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below.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 An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason.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 | 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 |
This record holds no relations between concepts. A layer is empty when the tagger recorded nothing in it — which is not the same as the paper having nothing to record.
| facet | tag | field | conf. | whose words |
|---|---|---|---|---|
| object_of_study | an open-access collection of published crystal structures, and the deposition machinery - identifiers, versioning, duplicate detection, validation - that lets a community keep one 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 | how to gather structural data that was historically split across three specialised databases into one searchable open collection, and keep it correct while it grows 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 | the COD itself at ~80,000 entries with near-full coverage of IUCr publications, plus a deposition pipeline that is described in enough detail to be re-implemented: permanent identifiers, Subversion revisions written into the file header, a four-condition duplicate rule ending in a human 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 | a scientific record split across databases by historical accident rather than by anything about the objects, and the identity problems that appear when the pieces are brought back together 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 | a permanent identifier is what makes citation possible and therefore must never change; a file that can never change cannot be corrected. The COD keeps the number fixed and versions the file underneath it, then writes both the revision and the repository address INTO the file, so that a copy taken away still says which state of which record it is Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[0] | 0.95 | the tagger's words |
| mechanisms | two measurements can agree to 0.5 A and 1.2 degrees and still be separate scientific facts; the COD only calls them duplicates if they also came from the same paper and the same pressure and temperature, and even then a person decides. The object does not determine its own key 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 | each CIF is given a full copy of the available bibliographic information rather than a pointer to it, so that the file can be processed and stored independently - the cost is duplication, and the benefit is that a file removed from the database is still interpretable Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[2] | 0.95 | the tagger's words |
| mechanisms | a structure on hold is present in the database with its cell constants, composition, symmetry and authorship visible and its COD number issued, while the coordinates - the part that could be scooped - are withheld until publication or one year, whichever comes first Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[3] | 0.95 | the tagger's words |
| limitations | the main functional limitation is the absence of a substructure search engine, because the chemical connectivity is not represented in the stored data 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 | chemical and hydrogen bond information is preserved only if the original file carried it, and is never inferred from the structure 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 | the deposition procedure has two manual steps - number assignment and error checking - and the number of determined structures is growing exponentially 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 | bibliographic information may fall back as far as the names of the directories the files arrived in 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 | one centralised repository is the authoritative source, and decentralisation is described as possible rather than done 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 | persistent URLs for deposited data are planned rather than in place 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 | software version control - Subversion, revision numbers, change logs, checkout of prior states - carried from programming practice into the curation of a scientific data record 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 | bulk distribution protocols from system administration - rsync, tarballs, anonymous repository checkout - used so that the database can be taken away entire rather than queried a record at a time 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 | every change to every file recorded in a central Subversion repository, with the revision and repository address written into the file header by software Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a silent edit - without the revision in the file, a corrected record and its predecessor are indistinguishable once either has been copied away · outcome: held | controls[0] | 0.95 | the tagger's words |
| controls | a four-condition duplicate scan - cell constants, angles, formula and same paper, plus pressure and temperature when given - with every candidate flagged for a person Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: numeric closeness alone deciding identity, and an automatic merge removing a second independent determination of the same compound · outcome: held | controls[1] | 0.95 | the tagger's words |
| controls | the whole collection, the database dumps and the web scripts published for anonymous checkout, so that any user can reconstitute the database and its logs locally Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the maintainers being the only witnesses to what the database contains and what was changed in it · outcome: held | controls[2] | 0.95 | the tagger's words |
| controls | each CIF checked for syntax by TWO independent parsers - the IUCr 'vcif' tool and a COD-written Perl parser Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: syntax errors in a deposited CIF, and the use of two independent parsers means an error has to be missed twice to get through · outcome (stated by the tagger, no quotation): held | controls[3] | 0.95 | the tagger's words |
| controls | validation that required data items - cell parameters, symmetry, bibliography - are present before deposition Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: depositions missing cell parameters, symmetry or bibliography - and note the verb: the CIFs 'can be' validated. The capability is described; the paper does not say it was run · outcome (stated by the tagger, no quotation): absent-declared-unreported | controls[4] | 0.95 | the tagger's words |
| controls | a fallback chain for bibliographic information ending, as a last resort, at the directory names the files arrived in Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: unattributed structures - though the paper is candid that the last resort is the directory name, which is the weakest link in the chain it describes · outcome (stated by the tagger, no quotation): held | controls[5] | 0.95 | the tagger's words |
| controls | each CIF given a full copy of the bibliographic information rather than a reference to it, so it can be processed independently Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a record that cannot be interpreted once separated from the collection it arrived in · outcome (stated by the tagger, no quotation): held | controls[6] | 0.95 | the tagger's words |
| controls | an on-hold deposition status releasing metadata and a COD number while withholding coordinates until publication or one year Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: depositors withholding structures altogether for fear of being scooped, at the cost of a delay the policy bounds · outcome (stated by the tagger, no quotation): held | controls[7] | 0.95 | the tagger's words |
| controls | chemical and hydrogen bond information preserved from the source file and never inferred from the structure Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a structure that cannot be identified as the compound it is, and bond information silently re-derived from geometry rather than taken from the depositor · outcome (stated by the tagger, no quotation): held | controls[8] | 0.95 | the tagger's words |
| controls | the claim that several dozen contributors are enough to provide qualified peer review for incoming structures Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: unreviewed structures reaching the database - conditional on adequate software and on enough volunteers, neither of which the paper claims to have · outcome (stated by the tagger, no quotation): absent-declared-unreported | controls[9] | 0.95 | the tagger's words |
| concepts | COD Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: COD | concepts[0] | 0.95 | the paper's words |
| concepts | duplicates Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: duplicates | concepts[1] | 0.95 | the paper's words |
| concepts | revision number Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: revision number | concepts[2] | 0.95 | the paper's words |
| concepts | cell constants Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: cell constants | concepts[3] | 0.95 | the paper's words |
| concepts | CIF Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: CIF | concepts[4] | 0.95 | the paper's words |
| concepts | substructure Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: substructure | concepts[5] | 0.95 | the paper's words |
| concepts | open-access Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: open-access | concepts[6] | 0.95 | the paper's words |
| concepts | mirrors Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: mirrors | concepts[7] | 0.95 | the paper's words |
| concepts | fragmentation Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: fragmentation | concepts[8] | 0.95 | the paper's words |
| senses | two entries being the SAME STRUCTURE - AS THE COD DEFINES IT: cell constants within 0.5 A, angles within 1.2 degrees, formulas matching, same paper, same pressure and temperature, and then a human agrees 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 | two entries being the SAME STRUCTURE - AS THE COD DELIBERATELY DOES NOT: a redetermination at higher precision or under different conditions gets a NEW identifier rather than replacing the old one 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 | a COD record's identity - THE COD NUMBER: permanent, assigned once, and never changed even when the file it names is corrected 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 | a COD record's identity - THE REVISION NUMBER: changes on every edit, is written into the file header by software, and is what makes any previous state recoverable 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 |
| senses | a deposited structure's visibility - UNDER THE ON-HOLD FLAG: cell constants, composition, symmetry and authorship are public and searchable Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[4] | 0.95 | the tagger's words |
| senses | a deposited structure's visibility - THE COORDINATES UNDER THE SAME FLAG: withheld until publication, or release by the authors, or one year Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[5] | 0.95 | the tagger's words |
| claim_relations | critiques → the historical three-way split of structural data across inorganic, metals and organic databases, which reflected how laboratories used to specialise rather than anything about the compounds 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 | extends → the IUCr's 2007 decision to make CIFs from its journals freely available to all databases, which is what let the COD download new structures routinely 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 | qualifies → its own functionality - without a representation of chemical connectivity there is no substructure search, which the authors call the main limitation 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 | qualifies → its own architecture - one centralised authoritative repository today, with decentralisation named as possible rather than implemented 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 |
| content_tags | A structure is a potential duplicate if its cell constants and angles fall within set tolerances, its formula matches and both come from the same paper; all potential duplicates are reviewed manually. 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 | a redetermination of the same compound is given a new identifier rather than replacing the old entry 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 | a permanent identifier and a mutable file need a second number, and the COD writes the revision and repository address into the file header 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 | chemical and hydrogen bonding is preserved only when the source file carried it and is never inferred from the structure 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 | An 'on hold' deposit shows cell constants, composition, symmetry and authorship and receives a COD number. 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 | The lack of a substructure search engine is one of the COD's main functional limitations. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[5] | 0.95 | the tagger's words |
| content_tags | the whole collection, its dumps and its scripts are available for anonymous checkout, so any user can reconstitute the database and read its deposition logs Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[6] | 0.95 | the tagger's words |
| content_tags | cell constants within 0.5 A and angles within 1.2 degrees of an existing entry, matching summary formulas, both structures published in the same paper, and identical pressure and temperature where specified - then reviewed manually Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: duplicates | content_tags.definitions[0] | 0.95 | the tagger's words |
| content_tags | a common group of atoms chemically linked in the same way - the paper's definition of chemical similarity, and the thing the database cannot search for Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: substructure | content_tags.definitions[1] | 0.95 | the tagger's words |
| content_tags | angstroms - the cell-constant tolerance inside which two entries become duplicate candidates 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 | degrees - the cell-angle tolerance in the same rule 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 | the length of a COD identifier, assigned once and never changed Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[2] | 0.95 | the tagger's words |
| content_tags | revision number Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: revision number | content_tags.variables[0] | 0.95 | the tagger's words |
Tags that could not be placed in the text:
What was deliberately not tagged, and why, is recorded per paper by the tagger. Where a paper has no such record, this page says so rather than implying that nothing was declined.