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# V3
V2 plus:
* [ ] wikipedia
* [ ] some unstrucutured refs
* [ ] OL
* [ ] weblinks
## Unstructured
* about 300M w/o title, etc.
* some docs mention a "doi" in "unstructured"
Possible extractable information:
* pages ranges with regex
* doi, isbn, issn
* author names with some NER?
* journal abbreviation
Numbers:
$ time zstdcat -T0 dataset-full-date-2021-02-20.json.zst | LC_ALL=C pv -l | LC_ALL=C grep -c -i "doi"
2772622
Sometimes, the key contains an ISBN:
```
"key":"9781108604222#EMT-rl-1_BIBe-r-213"
```
key with doi:
```
"index":63,"key":"10.1002/9781118960608.gbm01177-BIB6970|gbm01177-cit-6970","locator":"7
```
ISBN format:
* 978-9279113639
* 9781566773362
* 978-80-7357-299-0
URLs may be broken:
```
http://www. unaids.org/hivaidsinfo/statistics/fact_sheets/pdfs/Thailand_en.pdf
```
* 2030021 DOI
* 36376 arxiv
Some cases only contain authors and year, e.g.
```
{
"biblio": {
"contrib_raw_names": [
"W H Hartmann",
"B H Hahn",
"H Abbey",
"L E Shulman"
],
"unstructured": "Hartmann, W. H., Hahn, B. H., Abbey, H., and Shulman, L. E., Lancer, 1965, 1, 123.",
"year": 1965
},
```
Here, we could run a query, e.g.
https://fatcat.wiki/release/search?q=hahn+shulman+abbey+hartmann, and check for
result set size, year, etc.
Other example:
* https://fatcat.wiki/release/search?q=Goudie+Anderson+Gray+boyle+buchanan+year%3A1965
```
{
"biblio": {
"contrib_raw_names": [
"R B Goudie",
"J R Anderson",
"K G Gray",
"J A Boyle",
"W W Buchanar"
],
"unstructured": "Goudie, R. B., Anderson, J. R., Gray, K. G., Boyle, J. A., and Buchanar, W. W., ibid., 1965, 1, 322.",
"year": 1965
},
```
----
With `skate-from-unstructured` we get some more doi and arxiv identifiers from
unstructured refs (unstructured, key). How many?
```
$ time zstdcat -T0 dataset-full-date-2021-02-20.json.zst | pv -l | \
skate-from-unstructured | jq -rc 'select(.biblio.doi != null or .biblio.arxiv_id != null)' | wc -l
```
The https://anystyle.io/ CRF implementation seems really useful to parse out
the rest of the unstructured data.
* [ ] parse fields with some containerized anystyle (create an oci container
and somehow get it running w/ or w/o docker; maybe podman allows to run as
library?)
Example:
```
$ anystyle -f json parse xxxx.txt
[
{
"citation-number": [
"3. "
],
"author": [
{
"family": "JP",
"given": "Morgan"
},
{
"family": "CS",
"given": "Bailey"
}
],
"title": [
"Cauda equina syndrome in the dog: radiographical evaluation"
],
"volume": [
"21"
],
"pages": [
"45 – 58"
],
"type": "article-journal",
"container-title": [
"J Small Anim Practice"
],
"date": [
"1980"
]
}
]
```
Can dump the whole unstructured list in to a single file (one per line).
* 10K lines take: 32s
* 100M would take probably ~100h to parse.
----
* from 308 "UnmatchedRefs" we would extract doi/arxiv for 47696153.
Stats:
* 759,516,507 citation links.
* ~723,350,228 + 47,696,153
* 771046381 edges
----
* aitio has docker installed
```
Client:
Version: 17.06.0-ce
API version: 1.30
Go version: go1.8.3
Git commit: 02c1d87
Built: Fri Jun 23 21:23:31 2017
OS/Arch: linux/amd64
Server:
Version: 17.06.0-ce
API version: 1.30 (minimum version 1.12)
Go version: go1.8.3
Git commit: 02c1d87
Built: Fri Jun 23 21:19:04 2017
OS/Arch: linux/amd64
Experimental: false
```
Maybe build an alpine based image?
Both anystyle and grobid use wapiti under the hood; but they seem to differ
slightly. anystyle seems to be a smaller codebase overall. Grobid has an api
and various modes.
Note-to-self: Run a comparison between wapiti based citation extractors.
----
```
$ time zstdcat -T0 /magna/refcat/UnmatchedRefs/date-2021-02-20.json.zst | LC_ALL=C wc -l
260768384
```
----
# Wikipedia
* /magna/data/wikipedia_citations_2020-07-14
A first run only got 64008 docs; improbable that we are missing so many doi.
Also, need to generalize some skate code a bit.
|
