https://github.com/rdmpage/data-citation-corpus

Exploring the Data Citation Corpus
https://github.com/rdmpage/data-citation-corpus
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Exploring the Data Citation Corpus
Host: GitHub
URL: https://github.com/rdmpage/data-citation-corpus
Owner: rdmpage
Created: 2024-02-21T11:12:23.000Z (over 2 years ago)
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- Readme: README.md
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README

          # DataCite Citation Corpus

Exploring the [Data Citation Corpus](https://makedatacount.org/data-citation).

> A trusted central aggregate of all data citations to further our understanding of data usage and advance meaningful data metrics.

The data is available [by request](https://makedatacount.org/data-citation/#first-release), this repository documents my explorations of the data. (The data has subsequently been made freely available on Zenodo [doi:10.5281/zenodo.11196859](https://doi.org/10.5281/zenodo.11196859). )

Release announcement [DataCite launches first release of the Data Citation Corpus](https://makedatacount.org/first-release-of-the-open-global-data-citation-corpus/) doi:10.60804/r14z-mw10.

## Blog post

I wrote about the problems with the first release on iPhylo:

> Page, R. (2024). Problems with the DataCite Data Citation Corpus [https://doi.org/10.59350/t80g1-xys37](https://doi.org/10.59350/t80g1-xys37)

### Update(s)

#### Version 1.1

There is a simplified version (v1.1) of the data available on Zenodo, see [Data Citation Corpus first release Documentation](https://makedatacount.org/data-citation-corpus-documentation/#appendix).

I’m exploring adding this to CouchDB.

> DataCite, & Make Data Count. (2024). Data Citation Corpus Data File (v1.1) [Data set]. DataCite. [10.5281/zenodo.11216814](https://doi.org/10.5281/zenodo.11216814)

#### Version 2.0

Version 2.0 was released August 23, 2024 by Datacite [doi:10.5281/zenodo.13376773](https://doi.org/10.5281/zenodo.13376773)

> Data file for the second release of the Data Citation Corpus, produced by DataCite and Make Data Count as part of an ongoing grant project funded by the Wellcome Trust. Read more about the project.

> The data file includes 5,256,114 data citation records in JSON and CSV formats. The JSON file is the version of record.

## CouchDB (version 2)

Version two loaded into CouchDB using bulk upload, which is reasonably quick. The indexes take a while to build, and the JSON has a few issues, such as `title` field being present but empty.

## SQL version (first release of the data)

### Data extraction

`to_sql.php` parses the JSON data and outputs SQL statements to construct a simple SQL database to explore the data. 

### Sources

The data comes from two sources, DataCite and the Chan Zuckerberg Initiative (CSI):

```

SELECT COUNT(id), sourceId FROM citation GROUP BY sourceId;

```

### Repositories 

The data repositories cited are identified by local UUIDs, so it is non-trivial to figure out which repository is which. Here is a list so far:

| Repository | id | citation count |

|--|--|--|

| GenBank | 00363b65-f3ef-4fa9-8255-23ab269f4930| 3755354 |

| PDB | 87646104-e5ef-494b-b2f3-a46c9572e003| 1729783 |

| SNP | 6087b2e9-ecbf-4898-8047-5f484f1bce2f| 890431 |

| RefSeq | 1edec4bf-cfee-4296-8893-d1b0ca528f92 | 259548 | 

### Publishers

Publishers of the journals in which citations were found are also identified using UUIDs, the top twenty of these are listed below, and names can be determined by comparing with the chart on the [corpus dashboard](http://corpus.datacite.org/dashboard).

|name | citation count | publisherId|

|--|--|--|

| | 2136164 | e566bc45-b8bc-430c-ab2c-9c224e1c6f21|

| | 1029617 | ec75ceb1-215c-4376-aa1c-4b39d15dc069|

| | 938870 | 9ead11e4-bd7d-4c91-aff0-cb962676520a|

| | 768385 | bf7ba43c-7a3e-43e3-a9c2-6ed5b6fb6303|

| | 704427 | 08d58a61-189f-4316-892b-908a1832603d|

| | 635059 | babceab8-4440-4c65-ad12-24784190dbae|

| | 315654 | 602471f4-3d02-45f7-9d59-661471761299|

| | 312135 | af7d8efb-1a44-4a02-9d5b-29ceb6878117|

| | 277952 | |

| | 276263 | 37fa820b-d158-43b4-8f67-e0c2f7364d35|

| | 199813 | 55506166-9f8d-4685-967d-c71c7af956b7|

| | 171526 | 21c1aa14-7ac4-4ccb-8fdc-8f7e3ab047a9|

| | 147908 | 2189510e-6e8f-410c-bf2a-a92319d51b0e|

| | 114627 | faca9ac2-2c88-4277-acdd-0a1177c10094|

| | 98882 | deba021e-5d63-48af-82b5-673c6507a03e|

| | 97239 | dba2ef73-893b-4c93-9123-ea3429d6c983|

| | 92100 | cfd487dd-9342-49ec-b93a-a044da079368|

| | 90016 | bd7beb5b-5e4d-4c9f-b99d-944bc8cd5bf3|

| Pensoft | 80907 | 9d72fbd4-0a14-4ee8-bac5-75ec06ababf7|

| | 80376 | c6e65534-0e8c-495f-99ed-04ee78761d3c|

| | 60503 | d2c56596-551e-4f1e-81e6-d7bafe1670f8|

#### Protein Data Bank

The [Protein Data Bank](https://www.wwpdb.org) (PDB) has 1,729,783 citations in the corpus. There are 177,220 distinct PDB identifiers cited. 

```

SELECT DISTINCT UPPER(subjId) 

FROM citation 

WHERE repositoryId = '87646104-e5ef-494b-b2f3-a46c9572e003';

```

Running these through `pub_clean.php` 31,612 (18%) do not match the PDB pattern `/^[0-9][A-Za-z0-9]{3}$/`.

I downloaded a list of all PDB identifiers from https://files.wwpdb.org/pub/pdb/holdings/current_file_holdings.json.gz, and then loaded those identifiers into the table `identifier`. 

```

SELECT COUNT(id) FROM identifier WHERE namespace='pdb'; 

```

There are 216,225 distinct PDB identifiers.

We can compare the PDB identifiers in the corpus with the actual PDB identifiers:

```

SELECT COUNT(citation.id) FROM citation 

INNER JOIN identifier 

ON UPPER(citation.subjId) = identifier.id

WHERE repositoryId = '87646104-e5ef-494b-b2f3-a46c9572e003' AND identifier.namespace = 'pdb';

```

This finds 1,233,993 PDB identifiers, which is 71% of the total in the corpus. Hence a little under a third of the PDB citations appear to be erroneous.

We can look at some mistaken identifiers:

```

SELECT citation.id, UPPER(citation.subjId), identifier.id 

FROM citation 

LEFT JOIN identifier ON UPPER(citation.subjId) = identifier.id 

WHERE repositoryId = '87646104-e5ef-494b-b2f3-a46c9572e003' 

AND citation.subjId LIKE "1%"

AND identifier.id IS NULL

LIMIT 100;

```

#### GenBank

```

select distinct subjId from citation WHERE repositoryId = '00363b65-f3ef-4fa9-8255-23ab269f4930' limit 1000;

```

Run script `genbank.php` to test for occurrence in NCBI using `esummary` query.

#### RefSeq

1edec4bf-cfee-4296-8893-d1b0ca528f92, note that 7616 citations are to Creative Commons URLs(!)

### Repository identifiers 

#### Sources

|Label | Methodology | http://identifiers.org |

|--|--|--|

|arrayexpress | https://identifiers.org/arrayexpress:dataset | Y|

|biomodels | https://identifiers.org/biomodels.db:dataset | Y|

|bioproject | https://identifiers.org/bioproject:dataset | Y|

|biosample | https://identifiers.org/biosample:dataset | Y|

|biostudies | https://identifiers.org/biostudies:dataset | Y|

|cath | https://identifiers.org/cath:dataset | Y|

|chebi | https://identifiers.org/chebi:dataset[6:] | Y|

|chembl | https://identifiers.org/chembl:dataset | Y|

|complexportal | https://identifiers.org/complexportal:dataset | Y|

|dbgap | https://identifiers.org/dbgap:dataset | Y|

|doi | https://dx.doi.org/:dataset | sometimes|

|ebisc | https://cells.ebisc.org/dataset | N|

|efo | https://identifiers.org/efo:dataset | Y|

|ega | https://identifiers.org/ega.dataset:dataset | Y|

|emdb | https://identifiers.org/emdb:dataset | Y|

|empiar | https://identifiers.org/empiar:dataset | Y|

|ensembl | https://identifiers.org/ensembl:dataset  | Y|

|gca | https://identifiers.org/insdc.gca:dataset | Y|

|gen | https://identifiers.org/ena.embl:dataset | Y|

|geo | https://identifiers.org/geo:dataset | Y|

|gisaid | http://gisaid.org/EPI/dataset | N|

|go | https://identifiers.org/go:dataset | Y|

|hgnc | https://identifiers.org/hgnc:dataset | Y|

|hipsci | http://www.hipsci.org/lines/#/lines/dataset | N|

|hpa | https://identifiers.org/hpa:dataset | Y|

|igsr | https://identifiers.org/coriell:dataset | Y|

|intact | https://identifiers.org/intact:dataset | Y|

|interpro | https://identifiers.org/interpro:dataset | Y|

|metabolights | https://identifiers.org/metabolights:dataset | Y|

|metagenomics | https://identifiers.org/mgnify.samp:dataset | Y|

|mint | https://identifiers.org/mint:dataset | Y|

|omim | https://identifiers.org/mim:dataset | Y|

|orphadata | https://identifiers.org/orphanet:dataset | Y|

|pdb | https://identifiers.org/pdb:dataset | Y|

|pfam | https://identifiers.org/pfam:dataset | Y|

|pxd | https://identifiers.org/pride:dataset | Y|

|reactome | https://identifiers.org/reactome:dataset | Y|

|refseq | https://identifiers.org/refseq:dataset | Y|

|refsnp | https://identifiers.org/dbsnp:dataset | Y|

|rfam | https://identifiers.org/rfam:dataset | Y|

|rnacentral | https://identifiers.org/rnacentral:dataset | Y|

|rrid | https://identifiers.org/rrid:dataset | Y|

|treefam | https://identifiers.org/treefam:dataset | Y|

|uniparc | https://identifiers.org/uniparc:dataset | Y|

|uniprot | https://identifiers.org/uniprot:dataset | Y|

### Gotchas

Examples of problematic identifiers.

#### Text search fails to find identifier in article, even though it is there

The citation 10.1038/s42255-020-0213-x, SAMN11157311 seemed problematic as a simple search in the online text https://www.nature.com/articles/s42255-020-0213-x found no hits. Googling `SAMN11157311` turned up the PMC version of the paper [PMC7739959](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7739959/) and `SAMN11157311` is in Table 1. This table is not displayed in the article by default, instead it’s a clickable link https://www.nature.com/articles/s42255-020-0213-x/tables/1.

#### Specimen codes become accession numbers, figure captions become PDB records

See https://doi.org/10.3897%2FBDJ.4.e8032 for 126 citations that are all incorrect.

### Example citations

#### 127aac89-4568-4fab-83b0-ee03a4da7a16

http://127.0.0.1:5984/_utils/#database/data-citation-corpus-v2/127aac89-4568-4fab-83b0-ee03a4da7a16

```

{

  "_id": "127aac89-4568-4fab-83b0-ee03a4da7a16",

  "_rev": "1-0ed2a54e243ffbce5ebbf868f250d27b",

  "id": "127aac89-4568-4fab-83b0-ee03a4da7a16",

  "created": "2023-06-06T21:29:11.105+00:00",

  "updated": "2023-06-06T21:29:11.105+00:00",

  "repository": {

    "title": "© Georg Thieme Verlag",

    "external_id": null

  },

  "publisher": {

    "title": "Georg Thieme Verlag KG",

    "external_id": null

  },

  "journal": {

    "title": "Synlett",

    "external_id": null

  },

  "title": "Synthesis of (+)-Methyl Dihydropalustramate and of the Pyrido[1,2-a]azepine Core of Stemona Alkaloids",

  "dataset": "https://doi.org/10.4125/pd0066th",

  "publication": "https://doi.org/10.1055/s-0034-1380685",

  "publishedDate": "2015-04-30T00:00:00+00:00",

  "source": "datacite",

  "affiliations": [],

  "funders": [],

  "subjects": []

}

```

The repository and publisher are the same, in this case the cited data https://doi.org/10.4125/pd0066th (DataCite DOI) is the supplementary data for the article https://doi.org/10.1055/s-0034-1380685 (CrossRef), and both DOIs resolve to the same page. Not sure if this counts as “citation”.

#### fbd693f9-6278-4e39-9518-d06ab14072e7

http://127.0.0.1:5984/_utils/#database/data-citation-corpus-v2/fbd693f9-6278-4e39-9518-d06ab14072e7

```

  "title": "Binary black-hole simulation SXS:BBH:0229",

  "dataset": "https://doi.org/10.5281/zenodo.3274579",

  "publication": "https://doi.org/10.1088/0264-9381/33/16/165001",

```

Zenodo https://zenodo.org/records/3274579 describes this as:

```

Is supplement to

https://arxiv.org/abs/1904.04831 (URL)

10.1088/0264-9381/33/16/165001 (DOI)

```

and records no citations to the dataset. Again, this is not “citation”.
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