phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| 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— “The historical fragmentation of structural data into three databases covering inorganic compounds (Inorganic Crystal Structure Database; Belsky et al., 2002), metals, alloys and intermetallics (Crystal Data for Metals Database, CRYSTMET; White et al., 2002), and organic and organometallic small molecules (Cambridge Structural Database; Allen… | |
| claim-type | method— “Each CIF is checked for syntax errors, using both the publicly available ‘vcif’ tool from the IUCr (McMahon, 1998) and our own CIF parser written in Perl (http://www.perl.com/; Wall et al., 2000). Syntactic errors, if any, must be corrected manually; this task is currently performed by a COD maintainer responsible for deposition.” | |
| method — evidence | — “When all quality checks are passed, the existing COD database is scanned for duplicates. Duplicate structures are as a rule not deposited into the COD. A structure is considered a potential duplicate if its cell constants are within 0.5 Å and cell angles within 1.2° of any existing entry, the summary chemical formulas match, and both… | |
| object of study — evidence | — “The Crystallography Open Database (COD) is an ongoing initiative by crystallographers to gather all published inorganic, metal–organic and small organic molecule structures in one database, providing a straightforward search and retrieval interface. The COD adopts an open-access model for its >80 000 structure files.” | |
| research question — evidence | — “The historical fragmentation of structural data into three databases covering inorganic compounds (Inorganic Crystal Structure Database; Belsky et al., 2002), metals, alloys and intermetallics (Crystal Data for Metals Database, CRYSTMET; White et al., 2002), and organic and organometallic small molecules (Cambridge Structural Database; Allen… | |
| contribution — evidence | — “The Crystallography Open Database (COD) is an ongoing initiative by crystallographers to gather all published inorganic, metal–organic and… | |
| transfer | from software engineering: 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 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. | transfers[0] |
| transfer | from system administration: 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 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. | transfers[1] |
| mechanism | two numbers because one cannot do both jobs 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 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. | mechanisms[0] |
| mechanism | identity that is partly bibliographic 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 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. | mechanisms[1] |
| mechanism | a record made self-contained on purpose 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 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. | mechanisms[2] |
| mechanism | an embargo that splits the record rather than hiding it 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 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. | mechanisms[3] |
| 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 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] |
| 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 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] |
| 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 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] |
| qualifies | its own architecture - one centralised authoritative repository today, with decentralisation named as possible rather than implemented 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] |
| sense | 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 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. | senses[0] |
| sense | 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 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. | senses[1] |
| sense | 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 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. | senses[2] |
| sense | 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 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. | senses[3] |
| sense | a deposited structure's visibility - UNDER THE ON-HOLD FLAG: cell constants, composition, symmetry and authorship are public and searchable 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. | senses[4] |
| sense | 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 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. | senses[5] |
| control | every change to every file recorded in a central Subversion repository, with the revision and repository address written into the file header by software — 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 silent edit - without the revision in the file, a corrected record and its predecessor are indistinguishable once either has been copied away 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 | 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 — 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 numeric closeness alone deciding identity, and an automatic merge removing a second independent determination of the same compound 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 | 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 — 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 the maintainers being the only witnesses to what the database contains and what was changed in 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[2] |
| control | each CIF checked for syntax by TWO independent parsers - the IUCr 'vcif' tool and a COD-written Perl parser — held — rules out syntax errors in a deposited CIF, and the use of two independent parsers means an error has to be missed twice to get through 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 | validation that required data items - cell parameters, symmetry, bibliography - are present before deposition — absent-declared-unreported — rules out 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 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 | a fallback chain for bibliographic information ending, as a last resort, at the directory names the files arrived in — held — rules out 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 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 | each CIF given a full copy of the bibliographic information rather than a reference to it, so it can be processed independently — held — rules out a record that cannot be interpreted once separated from the collection it arrived in 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] |
| control | an on-hold deposition status releasing metadata and a COD number while withholding coordinates until publication or one year — held — rules out depositors withholding structures altogether for fear of being scooped, at the cost of a delay the policy bounds 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[7] |
| control | chemical and hydrogen bond information preserved from the source file and never inferred from the structure — held — rules out 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 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[8] |
| control | the claim that several dozen contributors are enough to provide qualified peer review for incoming structures — absent-declared-unreported — rules out unreviewed structures reaching the database - conditional on adequate software and on enough volunteers, neither of which the paper claims to have 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[9] |
| weight | 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 — 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. | claim_relations[0] |
| weight | 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 — 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 | its own functionality - without a representation of chemical connectivity there is no substructure search, which the authors call the main limitation — 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. | claim_relations[2] |
| weight | its own architecture - one centralised authoritative repository today, with decentralisation named as possible rather than implemented — 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[3] |
| 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. 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 — 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[1] |
| 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[2] |
| outcome (stated by the tagger, no quotation) | 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[3] |
| outcome (stated by the tagger, no quotation) | control — absent-declared-unreported 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 (stated by the tagger, no quotation) | 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 (stated by the tagger, no quotation) | 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] |
| outcome (stated by the tagger, no quotation) | 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[7] |
| outcome (stated by the tagger, no quotation) | 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[8] |
| outcome (stated by the tagger, no quotation) | control — absent-declared-unreported 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[9] |
| limitation | 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 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 | chemical and hydrogen bond information is preserved only if the original file carried it, and is never inferred from the structure 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 | the deposition procedure has two manual steps - number assignment and error checking - and the number of determined structures is growing exponentially 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 | bibliographic information may fall back as far as the names of the directories the files arrived in 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 | one centralised repository is the authoritative source, and decentralisation is described as possible rather than done 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 | persistent URLs for deposited data are planned rather than in place 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] |
| 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[5] |
| 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[6] |
| quantity | angstroms - the cell-constant tolerance inside which two entries become duplicate candidates 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 | degrees - the cell-angle tolerance in the same rule 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 | the length of a COD identifier, assigned once and never changed 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 | revision number 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] |
| definition | duplicates 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 | substructure 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] |
| concept | COD — not defined in this paper's own words; the Crystallography Open Database - an open-access collection of published structures, run by volunteers, mirrored, and downloadable in bulk 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 | duplicates — not defined in this paper's own words; two entries judged to be the same structure - defined here by four conjunctive conditions, one of which is bibliographic rather than physical, and settled by a person 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 | revision number — not defined in this paper's own words; the version-control identifier of a file's state, distinct from the permanent COD number that names the structure, and written into the file 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[2] |
| concept | cell constants — not defined in this paper's own words; the unit-cell lengths the duplicate rule is computed on, to a tolerance of 0.5 angstroms - the numeric half of an identity test whose other half is bibliographic 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 | CIF — not defined in this paper's own words; crystallographic information file - the master format in which the data is held, checked by two independent parsers before deposition 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 | substructure — not defined in this paper's own words; a group of atoms chemically linked in the same way; the similarity relation the database cannot search on, which the authors name as its main functional limitation 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 | open-access — not defined in this paper's own words; the model under which the whole collection, the database dumps and the web scripts can be checked out and reconstituted locally by anyone 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 | mirrors — not defined in this paper's own words; independent copies of the whole collection; possible because the data is open, and the reason a single authoritative repository is a choice rather than a necessity 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 | fragmentation — not defined in this paper's own words; the historical splitting of structural data across three specialised databases, which reflected how laboratories used to work rather than anything about the compounds 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] |
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.
Tag layer © the Meta-Tagging Project, CC BY 4.0. The paper text is © its authors/publisher
and is linked, not reproduced. Excerpts shown are short quotations for identification and verification.
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