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| -rw-r--r-- | python/notes/data/oci_v1_10_1056_nejmoa1606220.json | 5825 | ||||
| -rw-r--r-- | python/notes/data/oci_v1_10_1056_nejmoa1606220_lookup.json | 647 | ||||
| -rw-r--r-- | python/notes/data_quality.md | 11 | ||||
| -rw-r--r-- | python/notes/version_0.md | 468 | ||||
| -rw-r--r-- | python/notes/version_1.md | 491 | ||||
| -rw-r--r-- | python/notes/version_1_fuzzy_stats.txt | 30 | ||||
| -rw-r--r-- | python/notes/version_2.md | 219 | ||||
| -rw-r--r-- | python/notes/version_3.md | 187 | ||||
| -rw-r--r-- | python/notes/wikipedia_citations_2020-07-14.md | 51 |
9 files changed, 7929 insertions, 0 deletions
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+{"doi":"10.1007/978-3-030-54482-9_9","status":200} +{"doi":"10.1038/s41598-020-72088-2","status":200} +{"doi":"10.1002/cam4.3482","status":200} +{"doi":"10.1002/cam4.3341","status":200} +{"doi":"10.1007/s00345-020-03471-x","status":200} +{"doi":"10.1007/s00345-020-03485-5","status":200} +{"doi":"10.1007/s00345-020-03494-4","status":200} +{"doi":"10.17816/uroved102133-142","status":200} +{"doi":"10.1007/978-3-030-47963-3_27","status":200} +{"doi":"10.5694/mja2.50794","status":200} +{"doi":"10.3389/fonc.2020.01349","status":200} +{"doi":"10.3389/fonc.2020.564068","status":200} +{"doi":"10.3390/cells9112342","status":200} +{"doi":"10.2147/rru.s243088","status":200} +{"doi":"10.1097/coc.0000000000000721","status":200} +{"doi":"10.1007/s11934-020-00987-y","status":200} +{"doi":"10.1111/pin.13026","status":200} +{"doi":"10.1186/s12885-020-07276-4","status":200} +{"doi":"10.1186/s12885-020-07244-y","status":200} +{"doi":"10.1186/s13073-020-00770-1","status":200} +{"doi":"10.23736/s0393-2249.19.03637-3","status":200} +{"doi":"10.32322/jhsm.758558","status":404} +{"doi":"10.23736/s0393-2249.20.03780-7","status":200} +{"doi":"10.3310/hta24370","status":200} +{"doi":"10.1093/ndt/gfaa209","status":200} +{"doi":"10.23736/s0393-2249.20.03782-0","status":200} +{"doi":"10.1007/s41669-020-00226-7","status":200} +{"doi":"10.1007/s11701-020-01144-w","status":200} +{"doi":"10.1111/ctr.14080","status":200} +{"doi":"10.1002/pon.5513","status":200} +{"doi":"10.1259/bjr.20200571","status":200} +{"doi":"10.1259/bjr.20200848","status":200} +{"doi":"10.1002/pros.24075","status":200} +{"doi":"10.1007/978-3-662-61494-5_11","status":200} +{"doi":"10.1007/s00432-020-03327-2","status":200} +{"doi":"10.1111/ecc.13301","status":200} +{"doi":"10.1200/op.20.00508","status":200} +{"doi":"10.1038/s41443-020-00364-w","status":200} +{"doi":"10.1186/s12943-020-01264-9","status":200} +{"doi":"10.4103/iju.iju_115_20","status":200} +{"doi":"10.1007/978-3-319-57415-8_34","status":200} +{"doi":"10.2147/cmar.s257441","status":200} +{"doi":"10.1097/mou.0000000000000683","status":200} +{"doi":"10.1634/theoncologist.2018-0679","status":200} +{"doi":"10.1200/jco.19.01904","status":200} +{"doi":"10.1200/jco.19.02768","status":200} +{"doi":"10.1200/jco.19.02267","status":200} diff --git a/python/notes/data_quality.md b/python/notes/data_quality.md new file mode 100644 index 0000000..e386914 --- /dev/null +++ b/python/notes/data_quality.md @@ -0,0 +1,11 @@ +# Data quality issues + +## Mismatched PDFs + +* https://fatcat.wiki/release/iwvep44l5jdqlpwrzjmfdtxdrio + +Two SHA1, titles match roughly, but these are different docs: + +* [https://file.scirp.org/pdf/JSS_2017121115100474.pdf](https://file.scirp.org/pdf/JSS_2017121115100474.pdf) +* [http://eprints.lincoln.ac.uk/id/eprint/38840/1/polcice%20journal.pdf](http://eprints.lincoln.ac.uk/id/eprint/38840/1/polcice%20journal.pdf) + diff --git a/python/notes/version_0.md b/python/notes/version_0.md new file mode 100644 index 0000000..a6108be --- /dev/null +++ b/python/notes/version_0.md @@ -0,0 +1,468 @@ +# Version Zero Graph + +* ~1.8B refs +* ~250M w/ titles +* ~40M URLs +* ~25M titles exact match w/ fatcat + +``` +127589929 fatcat_lower.tsv +251934865 refs_lower.tsv + + 34931967 common_lower.tsv + 26840211 common.tsv +``` + +---- + +# Input + +Heavy intermediate schema from +[fatcat-scholar](https://git.archive.org/webgroup/fatcat-scholar/), raw names +of journal titles, partial metadata. + +Example line: + +```json +{ + "biblio": { + "contrib_raw_names": [ + "Maria Azevedo E Castro", + "Gabriela" + ], + "title": "Imaginação em Paul Ricoeur", + "unstructured": "AZEVEDO E CASTRO, Maria Gabriela. Imaginação em Paul Ricoeur." + }, + "index": 0, + "key": "b0", + "ref_source": "grobid", + "release_ident": "ruhcoyvxxnbc5ljsgtwhnolx3i", + "release_year": 2018, + "work_ident": "aaaes3j4argnjbkzdvud5r4zdi" +} +``` + +280M docs per file: + +``` +$ unpigz -c fatcat_scholar_work_fulltext.split_00.refs.json.gz | wc -l +285004451 +``` + +Around 1,733,267,886 total reference entries. Sample completeness (10M, 1M +docs, ...): + +``` +{ + "biblio": 10000000, + "biblio.arxiv_id": 23227, + "biblio.container_name": 5760760, + "biblio.contrib_raw_names": 7156385, + "biblio.doi": 3584451, + "biblio.issue": 763784, + "biblio.pages": 3331911, + "biblio.pmcid": 776, + "biblio.pmid": 471338, + "biblio.publisher": 398305, + "biblio.title": 5164864, + "biblio.unstructured": 6304402, + "biblio.url": 256771, + "biblio.volume": 5202508, + "biblio.year": 7055442, + "index": 10000000, + "key": 8986307, + "locator": 2390436, + "ref_source": 10000000, + "release_ident": 10000000, + "release_year": 9629380, + "target_release_id": 419033, + "work_ident": 10000000 +} +``` + +A smaller sample: + +``` +{ + "biblio": 1000000, + "biblio.arxiv_id": 1804, + "biblio.container_name": 580018, + "biblio.contrib_raw_names": 722526, + "biblio.doi": 355664, + "biblio.issue": 79145, + "biblio.pages": 337716, + "biblio.pmcid": 241, + "biblio.pmid": 47500, + "biblio.publisher": 39840, + "biblio.title": 518449, + "biblio.unstructured": 643743, + "biblio.url": 27535, + "biblio.volume": 526148, + "biblio.year": 713331, + "index": 1000000, + "key": 904205, + "locator": 241850, + "ref_source": 1000000, + "release_ident": 1000000, + "release_year": 966723, + "target_release_id": 42333, + "work_ident": 1000000 +} +``` + + +---- + +## DOI graph (v2020-01-22) + +* 615514019 lines joined + +We have "inbound" links for 41950903 records. + +However, the top ranked docs seem invalid, datasets from a few prefixes, mostly +from datacite. + +A few paper examples: + +* https://fatcat.wiki/release/6ykebula5vgtbinbqhftun7jcy + +> Effect of intensive blood-glucose control with metformin on complications in overweight patients with type 2 diabetes (UKPDS 34) + +* Google Scholar: [7981](https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=Effect+of+intensive+blood-glucose+control+with+metformin+on+complications+in+overweight+&btnG=) +* CG: 2105 + +---- + +* https://fatcat.wiki/release/3katpfxlafezdb2rmgoesgbhkq + +> The pyramid of corporate social responsibility + +* GS: [12690](https://scholar.google.com/scholar?cluster=13669080523806449819&hl=en&as_sdt=0,5&sciodt=0,5) +* CG: 2100 + +---- + +> Policy Paradigms, Social Learning, and the State + +* https://fatcat.wiki/release/m3kxbmcsxnfhzajp5zrdmvirlm +* GS: [8675](https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=Policy+Paradigms%2C+Social+Learning%2C+and+the+State&btnG=) +* CG: 2077 +* OCI: [2457](https://opencitations.net/index/coci/api/v1/citations/10.2307/422246) + +---- + +> Efficacy and safety of sorafenib in patients in the Asia-Pacific + +* GS: [4780](https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=%22Efficacy+and+safety+of+sorafenib+in+patients+in+the+Asia-Pacific%22&btnG=) +* CG: 1829 +* OCI: [2326](https://opencitations.net/index/coci/api/v1/citations/10.1016/s1470-2045(08)70285-7) + +---- + +* https://fatcat.wiki/release/qbdkrwg2dzbpfcdcsczy7ekjk4 +* GS: [4172](https://scholar.google.com/scholar?cluster=10863619180312621990&hl=en&as_sdt=0,5&sciodt=0,5) +* CG: 1303 +* OCI: [1776](https://opencitations.net/index/coci/api/v1/citations/10.1038/18884), 48, https://opencitations.net/browser/br/107462 + +---- + +> Oxidative stress and some antioxidant systems in acid rain-treated bean plants + +* https://fatcat.wiki/release/qrsuwvixbvgvpn4qzlum7btysi +* GS: [2613](https://scholar.google.com/scholar?cluster=13765746500938441584&hl=en&as_sdt=2005&sciodt=0,5) +* CG: 940 +* OCI: [1042](https://opencitations.net/index/coci/api/v1/citations/10.1016/s0168-9452(99)00197-1) + +Not sure, what this interface does, but it says "20" (?): +[https://opencitations.net/search?text=10.1016%2Fs0168-9452%2899%2900197-1&rule=doi](https://opencitations.net/search?text=10.1016%2Fs0168-9452%2899%2900197-1&rule=doi), https://opencitations.net/browser/br/808900 + +---- + +> Weak pairwise correlations imply strongly correlated network states in a neural population + +* https://fatcat.wiki/release/zga73tc25nabdpt42m5ehm2kmm +* GS: [1597](https://scholar.google.com/scholar?cluster=3499093978246315979&hl=en&as_sdt=0,5&sciodt=0,5) +* CG: 706 +* OCI: [794](https://opencitations.net/index/coci/api/v1/citations/10.1038/nature04701) + +---- + +* https://fatcat.wiki/release/fm3ni5ppyzbknj2ke3rcn3qwva +* GS: [3118](https://scholar.google.com/scholar?cluster=495710774871014506&hl=en&as_sdt=0,5&sciodt=0,5) +* CG: 679 +* OCI: [1092](https://opencitations.net/index/coci/api/v1/citations/10.1056/nejm199505183322008) + +---- + +* https://fatcat.wiki/release/5i5j4qejbjey5pt56n25qmxque +* GS: [1043](https://scholar.google.de/scholar?cluster=2106266772718631212&hl=en&as_sdt=2005&sciodt=0,5) +* CG: 421 +* OCI: [406](https://opencitations.net/index/coci/api/v1/citations/10.1029/2003wr002086) + +---- + +* https://fatcat.wiki/release/agrh573u7nc4hd5pmyptoasvua +* GS: [1391](https://scholar.google.de/scholar?cluster=17826621684475874878&hl=en&as_sdt=2005&sciodt=0,5) +* CG: 388 +* OCI: [444](https://opencitations.net/index/coci/api/v1/citations/10.1136/bjsm.2006.033548) + +---- + +* https://fatcat.wiki/release/ellwakbl7rdlvgqcu7d3ss7wwa +* GS: [593](https://scholar.google.com/scholar?cluster=537065614856795966&hl=en&as_sdt=2005&sciodt=0,5) +* CG: 315 +* OCI: [348](https://opencitations.net/index/coci/api/v1/citations/10.1038/nature05136) + +---- + +* https://fatcat.wiki/release/dj6pufwjnnhfvpwj7tuyfl43mq +* GS: [1948](https://scholar.google.com/scholar?q=A%20Simple%20Approximate%20Long-Memory%20Model%20of%20Realized%20Volatility) +* CG: 275 +* OCI: [336](https://opencitations.net/index/coci/api/v1/citations/10.1093/jjfinec/nbp001) + +## Refs completeness + +Use `ref_counter.py` and `ref_key_counter.py` to assess completeness of refs. + +Example (1.8B): + +```json +{ + "has_any_extid": 700483339, + "has_arxiv_id": 4229730, + "has_container_name": 998375407, + "has_container_volume_issue_pages": 99419112, + "has_contrib_container_year": 951540575, + "has_contrib_raw_names": 1243059610, + "has_doi": 620638102, + "has_index": 1682302484, + "has_issue": 132575565, + "has_key": 1559104305, + "has_locator": 415631451, + "has_pages": 578644324, + "has_pmcid": 129593, + "has_pmid": 80598430, + "has_publisher": 68809489, + "has_release_ident": 1733948346, + "has_release_year": 1671156907, + "has_target_release_id": 71771437, + "has_title": 895913346, + "has_title_container_year": 608802846, + "has_title_contrib_year": 800324815, + "has_unstructured": 1095871772, + "has_url": 44860180, + "has_volume": 901926534, + "has_work_ident": 1733948346, + "has_year": 1224602612, + "source_crossref": 716691444, + "source_datacite": 97088644, + "source_fatcat": 31681853, + "source_grobid": 778474113, + "source_pubmed": 110012292, + "total": 1733948346 +} +``` + +Overview of field cooccurences (running): + +```shell +$ zstdcat -T0 /bigger/scholar/fatcat_scholar_work_fulltext.refs.json.zst | pv -l | \ + parallel -j 16 --pipe --roundrobin python extra/ref_key_counter.py > ref_key_counter.json +$ python extra/ref_key_counter_merge.py < ref_key_counter.json +``` + +Top 3 key combinations: + +``` +$ jq -r '.c | to_entries[] | [.key, .value] | @tsv' ref_key_counter_merge.json | sort -nrk2,2 2> /dev/null | head -30 | column -t +container_name|contrib_raw_names|pages|title|unstructured|volume|year 259790699 +doi 257006166 +container_name|contrib_raw_names|issue|pages|title|unstructured|volume|year 82516807 +container_name|contrib_raw_names|doi|unstructured|volume|year 76858089 +pmid|unstructured 74462682 +container_name|contrib_raw_names|doi|title|volume|year 70821103 +container_name|contrib_raw_names|year 64064559 +container_name|contrib_raw_names|doi|volume|year 62559951 +unstructured 61711602 +contrib_raw_names|pages|title|unstructured|volume|year 61557246 +container_name|contrib_raw_names|volume|year 49701699 +container_name|contrib_raw_names|unstructured|volume|year 36401044 +contrib_raw_names|title|unstructured|year 35976833 +container_name|contrib_raw_names|doi|pages|title|unstructured|volume|year 32506970 +contrib_raw_names|publisher|title|unstructured|year 29668363 +container_name|contrib_raw_names|title|volume|year 27447296 +container_name|contrib_raw_names|unstructured|year 26663422 +container_name|contrib_raw_names|pages|title|unstructured|year 18216147 +contrib_raw_names|unstructured 16731608 +container_name|contrib_raw_names|title|unstructured|year 15103791 +doi|unstructured 14464285 +container_name|contrib_raw_names|doi|unstructured|year 14207167 +contrib_raw_names|pages|title|unstructured|year 14198485 +container_name|contrib_raw_names|doi|year 13159340 +contrib_raw_names|title|year 12980769 +contrib_raw_names|title|unstructured 12595768 +title|unstructured 12391968 +contrib_raw_names|title|volume|year 10636816 +container_name|contrib_raw_names|doi|title|year 10438502 +container_name|contrib_raw_names|pages|publisher|title|unstructured|year 8343539 +``` + +Loaded key sets and counts into sqlite3. + +``` +sqlite> select sum(count) from card; +1733948346 + +sqlite> select sum(count) from card where key like '%doi%' or key like '%pmid%' or key like '%pmcid%' or key like '%arxiv%'; +700483341 + +sqlite> select sum(count) from card where key like '%title%'; +895913346 + +sqlite> select sum(count) from card where key like '%doi%'; +620638104 + +sqlite3> select sum(count) from card where key like '%doi%' and key like '%title%'; +166109956 + +sqlite> select sum(count) from card where key like '%doi%' and key not like '%title%'; +454528148 + +sqlite> select sum(count) from card where key like 'unstructured'; +61711602 + +sqlite> select sum(count) from card where key not like '%pmid%' and key not like '%doi%' and key not like '%title%'; +309033306 + +sqlite> select * from card order by count desc limit 20; +container_name|contrib_raw_names|pages|title|unstructured|volume|year 259790699 +doi 257006166 +container_name|contrib_raw_names|issue|pages|title|unstructured|volum 82516807 +container_name|contrib_raw_names|doi|unstructured|volume|year 76858089 +pmid|unstructured 74462682 +container_name|contrib_raw_names|doi|title|volume|year 70821103 +container_name|contrib_raw_names|year 64064559 +container_name|contrib_raw_names|doi|volume|year 62559951 +unstructured 61711602 +contrib_raw_names|pages|title|unstructured|volume|year 61557246 +container_name|contrib_raw_names|volume|year 49701699 +container_name|contrib_raw_names|unstructured|volume|year 36401044 +contrib_raw_names|title|unstructured|year 35976833 +container_name|contrib_raw_names|doi|pages|title|unstructured|volume| 32506970 +contrib_raw_names|publisher|title|unstructured|year 29668363 +container_name|contrib_raw_names|title|volume|year 27447296 +container_name|contrib_raw_names|unstructured|year 26663422 +container_name|contrib_raw_names|pages|title|unstructured|year 18216147 +contrib_raw_names|unstructured 16731608 +container_name|contrib_raw_names|title|unstructured|year 15103791 + +sqlite> select * from card where key not like '%pmid%' and key not like '%doi%' and key not like '%title%' order by count desc limit 30; +container_name|contrib_raw_names|year|64064559 +unstructured|61711602 +container_name|contrib_raw_names|volume|year|49701699 +container_name|contrib_raw_names|unstructured|volume|year|36401044 +container_name|contrib_raw_names|unstructured|year|26663422 +contrib_raw_names|unstructured|16731608 +contrib_raw_names|unstructured|year|7668998 +container_name|year|4946373 +contrib_raw_names|pages|unstructured|4574398 +|3931030 +container_name|volume|year|3879804 +contrib_raw_names|year|3634698 +container_name|contrib_raw_names|2530058 +contrib_raw_names|pages|unstructured|volume|1963485 +container_name|contrib_raw_names|issue|unstructured|volume|year|1895141 +contrib_raw_names|pages|unstructured|volume|year|1825755 +contrib_raw_names|pages|unstructured|year|1759744 +contrib_raw_names|publisher|unstructured|year|1652931 +contrib_raw_names|1533772 +container_name|contrib_raw_names|volume|1183234 +year|1057837 +container_name|contrib_raw_names|issue|volume|year|857175 +contrib_raw_names|unstructured|volume|850630 +container_name|unstructured|year|842953 +contrib_raw_names|unstructured|url|year|764268 +contrib_raw_names|unstructured|url|644762 +contrib_raw_names|unstructured|volume|year|591568 +contrib_raw_names|publisher|unstructured|579832 +container_name|471755 +contrib_raw_names|pages|publisher|unstructured|year|402852 +``` + +## Refs as releases + +We convert refs to release like docs in order to run clustering on it. + +About 530M refs have to title, yet they have some kind of identifier (e.g. doi, +pmid, arxiv, ...). + +``` +$ zstdcat -T0 sha1-ef1756a5856085807742966f48d95b4cb00299a0.tsv.zst | LC_ALL=C grep -c -v -F "title" +529498074 +``` + +We have 895M refs with title. + +Rough metadata, extracted, partial or wrong, e.g "LANCET" as title. + +How many items have both title and `ext_ids` - via: + +``` +$ zstdcat -T0 with_title.json.zst | LC_ALL=C rg -c -F "ext_ids" +``` + +170985267 have both title and some identifier. + +Another performance data point: grepping through 300G on disk, uncompressed +takes about twice the time to uncompress (zstd) a 60G file on the fly. + +Sampling with `awk` - `cat 1B.txt | awk 'NR % 1000000 == 0'` + +## Ref only DOIs + +There are 2649552 unique strings identified as DOI in refs, which do not match +any DOI in fatcat (normalized to lowercase). However, a link check of a sample +of 2K reveals that only 20% of those DOI actually resolve. + +There may be around 500K DOI in references that do not appear in fatcat. + +## Fuzzy matches + +* [x] convert refs docs into partial release entities +* [x] concatenate with fatcat releases +* [-] cluster; note: huge file, stopped + +Ran a sample on 11M (1.4G compressed) docs (10M refs, 1M fatcat), clustered in +18min. + +Found 15214 clusters, but all with fatcat, not refs/fatcat. Need to extend the dataset size. + +Running sample with 110M docs (100M refs, 10M fatcat; 14G compressed; clustered +96min); found 231998 clusters, but again none between the refs and fatcat +groups. + +## Quality observations + +A case, where we seem to have GROBID output in the refs dataset, from a PDF, which does not fit the PDF linked: + +* https://fatcat.wiki/release/5al5q6ksx5dxhhtmt4cjajehge (should be an article, 157-187), but: +* [https://smartech.gatech.edu/bitstream/handle/1853/26610/zhang_lei_200812_phd.pdf](https://smartech.gatech.edu/bitstream/handle/1853/26610/zhang_lei_200812_phd.pdf) is a thesis (150+ pages) + +## Approximate string match + +* in refs: "Turkish Cypriots fear implications of Cyprus EU presidency" - but + we have: https://fatcat.wiki/release/vp4h6jp65bfuro2wrkh3qg3ody, "Turkey's +boycott of the Cyprus EU presidency" plus duplication. We would need an approx. string match, or substring match. + + +# Lookup storage + +* Can we convert our JSON into parquet for faster queries? Should we index by + release? By title? + +# Funnel Setup + +* [ ] refs with a DOI (620,638,104); lookup the DOI; keep (refrid, rid) +* [ ] refs with other extids; lookup id in extracted lists from fatcat +* [ ] refs w/o extids, but with a title + diff --git a/python/notes/version_1.md b/python/notes/version_1.md new file mode 100644 index 0000000..50a38cc --- /dev/null +++ b/python/notes/version_1.md @@ -0,0 +1,491 @@ +# Version 1 + +Includes: + +* doi, pmid, pmcid, arxiv +* title-lower exact matches + +Title join yields 16B+ matches (16761492658), since we have many generic rows, e.g. +"introduction". 180G compressed, about 53 min for a one pass. + +``` +$ LC_ALL=C time join -t ' ' -1 2 -2 2 <(zstdcat FatcatTitlesLower/sha1-ef1756a5856085807742966f48d95b4cb00299a0.tsv.zst) \ + <(zstdcat RefsTitlesLower/sha1-ef1756a5856085807742966f48d95b4cb00299a0.tsv.zst) | zstd -c > title.tsv.zst +``` + +Filter and sample with `awk`, e.g. via: + +``` +$ zstdcat -T0 title.tsv.zst | LC_ALL=C grep -E '^[[:alnum:]]' | awk 'length($1) > 30' | awk 'NR%1000==0' +``` + +Need to pre-filter before join, to keep join smaller. + +Basic inspection of the "exact lower title" set. + +* 16B+ candidates +* as the join keys are already sorted, we can run uniq + +``` +$ time zstdcat -T0 title.tsv.zst | LC_ALL=C cut -f 1 | LC_ALL=C pv -l | LC_ALL=C uniq -c | zstd -c > title_counts.tsv.zst + +real 92m28.442s +user 142m49.627s +sys 46m9.473s +``` + +Some manual sampling: + +Different release, but same references (585): + +* https://fatcat.wiki/release/zvd5r6grcvd6tnmeovijvx4soq/references +* https://fatcat.wiki/release/4zutv5pmhjgs7nfvqy2zws6icm/references + +There are duplicates in the join, need to filter them out. + +``` +$ time zstdcat -T0 title.tsv.zst | LC_ALL=C uniq | LC_ALL=C pv -l | zstd -T0 -c > title_uniq.tsv.zst +``` + +Left with about 13B uniq. + +OCI, example: + +* https://opencitations.net/index/coci/api/v1/citations/10.1056/nejmoa1606220 +* OCI: 646 citations + +we have 356 via doi, pmid, about 112 via title, 468 total; which one do we miss? + +However, we do have all but one of the OCI DOIs in fatcat: + +``` +$ jq -r '.[].citing' oci_v1_10_1056_nejmoa1606220.json | tigris-doi > oci_v1_10_1056_nejmoa1606220_lookup.json +``` + +Example, DOI not in OCI: + +* https://opencitations.net/index/coci/api/v1/citations/10.14236/ewic/eva2014.30 + +Possible mitigations: + +* ignore common titles +* ignore numbers only + +Examples: `42` appeards 3816 times + +Harder cases: + +* "41st annual meeting" - too generic, and wrong + + +Generic DOI lookup from OCI in fatcat: + +``` +$ curl -sL https://opencitations.net/index/coci/api/v1/citations/10.1016/j.cell.2010.03.012 | jq -rc '.[].citing' | tigris-doi -w 256 | jq -rc . +{"doi":"10.1530/erc-16-0228","status":200} +{"doi":"10.1371/journal.pone.0080023","status":200} +{"doi":"10.1074/jbc.m114.566141","status":200} +... +``` + +Overall: + +* 31344136 unique titles + +most common join title: + +* 11,939,631,644 introduction +* also: "science", "preface", "book reviews", ..., "cell", ... + +Filtering: + +``` +$ zstdcat -T0 title_counts.tsv.zst | \ + LC_ALL=C awk '($1 > 5000 && length($0) < 30) || ($1 > 15000 && length($0) < 40)' +``` + +About 7275 titles to filter out, e.g. + +``` +... + 475300 abstracts of papers + 20502 ac + 13892 aca + 7881 academic freedom +... + 5047 community policing + 157176 community-acquired pneumonia + 68222 commutative algebra + 5512 comorbidity + 5516 compact stars + 8865 company +... + 7353 facebook + 6461 facial pain + 8977 facilities + 5238 facing the future + 5064 fact + 11198 fact sheet +... +``` + +Trying fuzzycat clustering, with 0.1.13, which allows to compress `-C` +intermediate artifacts. + +``` +$ time zstdcat \ + RefsReleasesMerged/sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst | \ + parallel -j 16 --block 10M --roundrobin --pipe 'TMPDIR=/bigger/tmp python -m \ + fuzzycat cluster -t tsandcrawler -C' | pv -l | zstd -T0 -c > cluster.ndj.zst +``` + +Using fuzzycat 0.1.13 with compression; all fine until: + +``` +$ time zstdcat \ + RefsReleasesMerged/sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst | pv \ + -l | parallel -j 16 --block 10M --roundrobin --pipe 'TMPDIR=/bigger/tmp python \ + -m fuzzycat clust er -t tsandcrawler -C' | zstd -T0 -c > cluster.ndj.zst + +1.58G 6:35:39 [66.5k/s] [ <=> ] +parallel: Error: Output is incomplete. +parallel: Error: Cannot append to buffer file in /tmp. +parallel: Error: Is the disk full? +parallel: Error: Change $TMPDIR with --tmpdir or use --compress. + +real 1013m20.128s +user 2696m14.290s +sys 119m29.419s +``` + +A run with `--compress` and `--tmpdir` set on parallel worked: + +``` +$ time zstdcat + RefsReleasesMerged/sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst | + parallel --compress --tmpdir /fast/tmp -j 4 --block 10M --roundrobin --pipe + 'TMPDIR=/bigger/tmp python -m fuzzycat cluster -t tsandcrawler -C' | + zstd -T0 -c > cluster.ndj.zst + +real 1301m26.206s +user 2778m20.635s +sys 140m32.121s +``` + +* 21h, finds 5850385 clusters (seems too low) + +# Sample generation + +Created samples, filtered by years (1895, 1955, 1995, 2015) for refs and releases: + +* ~114M refs +* ~7M releases + +Adjusted `tasks.py` to use a different sha1 and updated settings.ini with +sample file locations. + +# First clustering + +Key extraction (KE), sorting and clustering took 14h, when the merged dataset +is already there (it takes ~80min to convert refs to releases, plus a bit more +to concatenate the files). + +``` +$ ./run.sh RefsFatcatClusters + +real 841m45.169s +user 2872m35.481s +sys 561m14.231s +``` + +Resulting file is 154G compressed. + +Cluster count and sizes: + +``` +$ zstdcat -T0 sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst | \ + LC_ALL=C pv -l | LC_ALL=C jq -rc '[(.v|length), .k] | @tsv' > sizes.tsv +``` + +Follow up tasks: + +* each cluster will have ref and non-ref items +* we want at least one non-ref item + +``` +$ skate-cluster -both ... +``` + +Will keep only those clusters that contain at least one ref and one non-ref +entry. + +Found 40257623 clusters, iteration over the 89GB compressed file takes 28min. + +Raw synopsis: + +``` +$ zstdcat sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst | \ + jq -c -C 'select(.v|length == 2) | [(.v[] | [.ext_ids.doi[0:2], .title[0:10], .ident, .extra.skate.status == "ref"])]' | less -r +``` + +Some numbers: + +* [ ] number of 2-clusters, where not both entries have a doi? + +Verification. + +* needed a different batch verifier, since we do not need pairwise comparisons; + +``` +$ cut -d ' ' -f 3-4 cluster_ref_verify.tsv | LC_ALL=C sort -S20% | uniq -c | sort -nr +8390899 Status.DIFFERENT Reason.YEAR +6191622 Status.EXACT Reason.DOI +5468805 Status.STRONG Reason.JACCARD_AUTHORS +3848964 Status.DIFFERENT Reason.CONTRIB_INTERSECTION_EMPTY +3306728 Status.STRONG Reason.SLUG_TITLE_AUTHOR_MATCH +1263329 Status.STRONG Reason.TOKENIZED_AUTHORS + 424441 Status.AMBIGUOUS Reason.UNKNOWN + 199157 Status.EXACT Reason.TITLE_AUTHOR_MATCH + 138144 Status.AMBIGUOUS Reason.SHORT_TITLE + 92054 Status.DIFFERENT Reason.PAGE_COUNT + 25122 Status.AMBIGUOUS Reason.BLACKLISTED + 22964 Status.EXACT Reason.WORK_ID + 17702 Status.STRONG Reason.VERSIONED_DOI + 16236 Status.DIFFERENT Reason.COMPONENT + 14462 Status.STRONG Reason.PREPRINT_PUBLISHED + 9632 Status.STRONG Reason.PMID_DOI_PAIR + 3429 Status.STRONG Reason.ARXIV_VERSION + 3288 Status.STRONG Reason.CUSTOM_IEEE_ARXIV + 729 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_5860_CHOICE_REVIEW + 195 Status.STRONG Reason.FIGSHARE_VERSION + 76 Status.DIFFERENT Reason.CUSTOM_IOP_MA_PATTERN + 74 Status.DIFFERENT Reason.TITLE_FILENAME + 43 Status.DIFFERENT Reason.NUM_DIFF + 22 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_7916 + 11 Status.AMBIGUOUS Reason.BLACKLISTED_FRAGMENT + 1 Status.STRONG Reason.CUSTOM_BSI_UNDATED +``` + +Guessing: Maybe 30% "strong", so maybe ~120M new edges? + + +---- + +# Manual sampling and issues + +``` +https://fatcat.wiki/release/tiqp3w67sjhzdorc6whizpnbyy https://fatcat.wiki/release/lbmqfamyoveldeyvv5xktq5ayi Status.DIFFERENT Reason.YEAR +``` + +Grobid output: + +```xml +<biblStruct xml:id="b77"> + <analytic> + <title level="a" type="main">The Social Construction of Planning Systems: A Strategic-Relational Institutionalist Approach</title> + <author> + <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">L</forename><surname>Servillo</surname></persName> + </author> + <author> + <persName xmlns="http://www.tei-c.org/ns/1.0"><surname>Van Den</surname></persName> + </author> + <author> + <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">P</forename><surname>Broeck</surname></persName> + </author> + <idno type="DOI">10.1080/02697459.2012.661179></idno> + <idno>En línea] 2012 [Fecha de consulta: 21 de agosto 2015</idno> + <ptr target="<http://dx.doi.org/10.1080/02697459.2012.661179>" /> + </analytic> + <monogr> + <title level="j">En: Planning Practice and Research</title> + <imprint> + <biblScope unit="volume">27</biblScope> + <biblScope unit="issue">1</biblScope> + <biblScope unit="page" from="41" to="61" /> + </imprint> + </monogr> +</biblStruct> +``` + +There are dates, but not explicit clean 2012. + +Another issue: + +``` +https://fatcat.wiki/release/2n7pyugxenb73gope52bn6m2ru https://fatcat.wiki/release/p4bettvcszgn5d3zls5ogdjk4u Status.STRONG Reason.SLUG_TITLE_AUTHOR_MATCH +``` + +Very similar titles: + +"... nephrotic syndrome in childhood" vs "... nephrotic syndrome in childred" ... + +* year do not match, but fuzzycat does not check from that (1995, vs 2004 in the refs) + +Intermediate match results: + +``` +141970958 Status.DIFFERENT Reason.YEAR +106734288 Status.EXACT Reason.DOI + 91205561 Status.STRONG Reason.JACCARD_AUTHORS + 66894403 Status.DIFFERENT Reason.CONTRIB_INTERSECTION_EMPTY + 53693804 Status.STRONG Reason.SLUG_TITLE_AUTHOR_MATCH + 20889423 Status.STRONG Reason.TOKENIZED_AUTHORS + 7449880 Status.AMBIGUOUS Reason.UNKNOWN + 3507120 Status.EXACT Reason.TITLE_AUTHOR_MATCH + 1199761 Status.DIFFERENT Reason.PAGE_COUNT + 1121611 Status.AMBIGUOUS Reason.SHORT_TITLE + 395710 Status.EXACT Reason.WORK_ID + 362089 Status.DIFFERENT Reason.COMPONENT + 351654 Status.AMBIGUOUS Reason.BLACKLISTED + 326730 Status.STRONG Reason.VERSIONED_DOI + 239924 Status.STRONG Reason.PREPRINT_PUBLISHED + 171594 Status.STRONG Reason.PMID_DOI_PAIR + 54646 Status.STRONG Reason.ARXIV_VERSION + 49248 Status.STRONG Reason.CUSTOM_IEEE_ARXIV + 17135 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_5860_CHOICE_REVIEW + 5219 Status.DIFFERENT Reason.TITLE_FILENAME + 2451 Status.AMBIGUOUS Reason.APPENDIX + 1874 Status.STRONG Reason.FIGSHARE_VERSION + 1231 Status.DIFFERENT Reason.CUSTOM_IOP_MA_PATTERN + 774 Status.DIFFERENT Reason.NUM_DIFF + 448 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_7916 + 123 Status.AMBIGUOUS Reason.BLACKLISTED_FRAGMENT + 17 Status.STRONG Reason.CUSTOM_BSI_UNDATED + 17 Status.DIFFERENT Reason.CUSTOM_PREFIX_10_14288 + 6 Status.STRONG Reason.CUSTOM_BSI_SUBDOC +``` + +Another false negative: + +* https://fatcat.wiki/release/sqrld55t4zdrhf23oq75azo67a +* http://real.mtak.hu/78943/1/acs.jctc.8b00072.pdf, https://fatcat.wiki/release/gx7owpu4gbcglfwlyzdh5qlfji + +``` +https://fatcat.wiki/release/sqrld55t4zdrhf23oq75azo67a https://fatcat.wiki/release/gx7owpu4gbcglfwlyzdh5qlfji Status.DIFFERENT Reason.YEAR +``` + +Both docs contain 1972? + +```xml +<biblStruct xml:id="b67"> + <analytic> + <title level="a" type="main">Variational Wavefunctions for H2 +</title> + <author> + <persName xmlns="http://www.tei-c.org/ns/1.0"><forename type="first">F</forename><surname>Weinhold</surname></persName> + </author> + </analytic> + <monogr> + <title level="j">J. Chem. Phys</title> + <imprint> + <biblScope unit="volume">56</biblScope> + <biblScope unit="page" from="3798" to="3801" /> + <date type="published" when="1972" /> + </imprint> + </monogr> +</biblStruct> +``` + +---- + +Running: + +``` +$ time zstdcat -T0 sha1-ef1756a5856085807742966f48d95b4cb00299a0.json.zst | parallel --tmpdir /bigger/tmp --blocksize 4M --pipe -j 16 'python -m fuzzycat verify_ref' > clus +ter_ref_verify.tsv +``` + +resulted in a 69GB tsv file and took 3056m5.322s (~50h), 512033197 comparisons. + +Stats: + +``` +$ TMPDIR=/bigger/tmp LC_ALL=C time zstdcat -T0 + cluster_ref_verify_2021_02_16.tsv.zst | cut -d ' ' -f 3-4 | TMPDIR=/bigger/tmp + LC_ALL=C sort -S20% | uniq -c | sort -nr + +146095427 Status.DIFFERENT Reason.YEAR +110052214 Status.EXACT Reason.DOI + 94300998 Status.STRONG Reason.JACCARD_AUTHORS + 68986574 Status.DIFFERENT Reason.CONTRIB_INTERSECTION_EMPTY + 55199653 Status.STRONG Reason.SLUG_TITLE_AUTHOR_MATCH + 21545821 Status.STRONG Reason.TOKENIZED_AUTHORS + 7746937 Status.AMBIGUOUS Reason.UNKNOWN + 3626713 Status.EXACT Reason.TITLE_AUTHOR_MATCH + 1265506 Status.DIFFERENT Reason.PAGE_COUNT + 1171178 Status.AMBIGUOUS Reason.SHORT_TITLE + 409043 Status.EXACT Reason.WORK_ID + 374051 Status.DIFFERENT Reason.COMPONENT + 356772 Status.AMBIGUOUS Reason.BLACKLISTED + 336588 Status.STRONG Reason.VERSIONED_DOI + 249723 Status.STRONG Reason.PREPRINT_PUBLISHED + 177547 Status.STRONG Reason.PMID_DOI_PAIR + 56445 Status.STRONG Reason.ARXIV_VERSION + 51776 Status.STRONG Reason.CUSTOM_IEEE_ARXIV + 17887 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_5860_CHOICE_REVIEW + 5255 Status.DIFFERENT Reason.TITLE_FILENAME + 2451 Status.AMBIGUOUS Reason.APPENDIX + 1946 Status.STRONG Reason.FIGSHARE_VERSION + 1263 Status.DIFFERENT Reason.CUSTOM_IOP_MA_PATTERN + 798 Status.DIFFERENT Reason.NUM_DIFF + 463 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_7916 + 125 Status.AMBIGUOUS Reason.BLACKLISTED_FRAGMENT + 18 Status.STRONG Reason.CUSTOM_BSI_UNDATED + 18 Status.DIFFERENT Reason.CUSTOM_PREFIX_10_14288 + 7 Status.STRONG Reason.CUSTOM_BSI_SUBDOC + +``` + +286M positive links. + +``` +$ grep -E "Status.STRONG|Status.EXACT" version_1_fuzzy_stats.txt | awk '{print $1}' | paste -sd+ | bc +286008492 +``` + +Or 175M, if we exclude DOI and work matches. + +``` +$ grep -E "Status.STRONG|Status.EXACT" version_1_fuzzy_stats.txt | grep -Ev "Reason.DOI|Reason.WORK_ID" | awk '{print $1}' | paste -sd+ | bc +175547235 +``` + +---- + +The final derivation dep tree looks like: + +``` + $ ./tasks.py -d BiblioRef + \_ BiblioRef(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ BiblioRefFuzzy(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ RefsFatcatClusterVerify(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ RefsFatcatClusters(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ RefsFatcatSortedKeys(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ RefsReleasesMerged(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ ReleaseExportExpanded() + \_ RefsToRelease(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ Input() + \_ BiblioRefFromJoin(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ RefsFatcatGroupJoin(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ RefsFatcatPMCIDJoin(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ RefsPMCID(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ Input() + \_ FatcatPMCID(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ ReleaseExportExpanded() + \_ RefsFatcatArxivJoin(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ FatcatArxiv(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ ReleaseExportExpanded() + \_ RefsArxiv(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ Input() + \_ RefsFatcatPMIDJoin(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ FatcatPMID(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ ReleaseExportExpanded() + \_ RefsPMID(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ Input() + \_ RefsFatcatDOIJoin(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ FatcatDOIsLower(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ FatcatDOIs(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ ReleaseExportExpanded() + \_ RefsDOIsLower(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ RefsDOIs(sha1=ef1756a5856085807742966f48d95b4cb00299a0) + \_ Input() +``` diff --git a/python/notes/version_1_fuzzy_stats.txt b/python/notes/version_1_fuzzy_stats.txt new file mode 100644 index 0000000..210fc0b --- /dev/null +++ b/python/notes/version_1_fuzzy_stats.txt @@ -0,0 +1,30 @@ +146095427 Status.DIFFERENT Reason.YEAR +110052214 Status.EXACT Reason.DOI +94300998 Status.STRONG Reason.JACCARD_AUTHORS +68986574 Status.DIFFERENT Reason.CONTRIB_INTERSECTION_EMPTY +55199653 Status.STRONG Reason.SLUG_TITLE_AUTHOR_MATCH +21545821 Status.STRONG Reason.TOKENIZED_AUTHORS +7746937 Status.AMBIGUOUS Reason.UNKNOWN +3626713 Status.EXACT Reason.TITLE_AUTHOR_MATCH +1265506 Status.DIFFERENT Reason.PAGE_COUNT +1171178 Status.AMBIGUOUS Reason.SHORT_TITLE + 409043 Status.EXACT Reason.WORK_ID + 374051 Status.DIFFERENT Reason.COMPONENT + 356772 Status.AMBIGUOUS Reason.BLACKLISTED + 336588 Status.STRONG Reason.VERSIONED_DOI + 249723 Status.STRONG Reason.PREPRINT_PUBLISHED + 177547 Status.STRONG Reason.PMID_DOI_PAIR + 56445 Status.STRONG Reason.ARXIV_VERSION + 51776 Status.STRONG Reason.CUSTOM_IEEE_ARXIV + 17887 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_5860_CHOICE_REVIEW + 5255 Status.DIFFERENT Reason.TITLE_FILENAME + 2451 Status.AMBIGUOUS Reason.APPENDIX + 1946 Status.STRONG Reason.FIGSHARE_VERSION + 1263 Status.DIFFERENT Reason.CUSTOM_IOP_MA_PATTERN + 798 Status.DIFFERENT Reason.NUM_DIFF + 463 Status.AMBIGUOUS Reason.CUSTOM_PREFIX_10_7916 + 125 Status.AMBIGUOUS Reason.BLACKLISTED_FRAGMENT + 18 Status.STRONG Reason.CUSTOM_BSI_UNDATED + 18 Status.DIFFERENT Reason.CUSTOM_PREFIX_10_14288 + 7 Status.STRONG Reason.CUSTOM_BSI_SUBDOC + diff --git a/python/notes/version_2.md b/python/notes/version_2.md new file mode 100644 index 0000000..873b5bf --- /dev/null +++ b/python/notes/version_2.md @@ -0,0 +1,219 @@ +# Version 2 (2021-02-18) + +As target document we want, as per `proposals/2021-01-29_citation_api.md` the following: + +``` +BiblioRef ("bibliographic reference") + _key: Optional[str] elasticsearch doc key + ("release", source_release_ident, ref_index) + ("wikipedia", source_wikipedia_article, ref_index) + update_ts: Optional[datetime] elasticsearch doc timestamp + + # metadata about source of reference + source_release_ident: Optional[str] + source_work_ident: Optional[str] + source_wikipedia_article: Optional[str] + with lang prefix like "en:Superglue" + # skipped: source_openlibrary_work + # skipped: source_url_surt + source_release_stage: Optional[str] + source_year: Optional[int] + + # context of the reference itself + ref_index: int + 1-indexed, not 0-indexed + ref_key: Optional[str] + eg, "Lee86", "BIB23" + ref_locator: Optional[str] + eg, page number + + # target of reference (identifiers) + target_release_ident: Optional[str] + target_work_ident: Optional[str] + target_openlibrary_work: Optional[str] + target_url_surt: Optional[str] + target_url: Optional[str] + would not be stored in elasticsearch, but would be auto-generated + by all "get" methods from the SURT, so calling code does not need + to do SURT transform + # skipped: target_wikipedia_article + + match_provenance: str + crossref, pubmed, grobid, etc + match_status: Optional[str] + strong, weak, etc + TODO: "match_strength"? + match_reason: Optional[str] + "doi", "isbn", "fuzzy title, author", etc + maybe "fuzzy-title-author"? + + target_unstructured: string (only if no release_ident link/match) + target_csl: free-form JSON (only if no release_ident link/match) + CSL-JSON schema (similar to ReleaseEntity schema, but not exactly) + generated from unstructured by a GROBID parse, if needed +``` + +This resulting docs/index will be generated from various pipelines: + +* various identifier joins (doi, pmid, pmcid, arxiv, ...) +* a fuzzy matching pipeline +* a wikipedia "scan" over publications, by DOI, title, direct link +* an open library "scan", matching possibly ISBN or book titles against the catalog +* relating a source document to all its referenced web pages (as `target_url`) + +The raw inputs: + +* release export (expanded or minimized) +* an aggregated list of references +* wikipedia dumps, e.g. en, de, fr, es, ... +* an openlibrary dump +* auxiliary data structures, e.g. journal name lookup database (abbreviations), etc. +* MAG, base, aminer, and other datasets to run comparisons against + +# Setup and deployment + +* [-] clone this repo +* [x] copy "zipapp" +* [x] setup raw inputs in settings.ini +* [x] run task + +Using shiv for creating single-file deployment. Single config file. Handle to +list and inspect files. Keep it minimal. External tools in skate. + +---- + +# Match with more complete data + +* [x] more sensible changing between inputs (e.g. sample, full, etc.) + +For joins. + +* [x] reduce release entities to minimum (ReleaseEntityReduced) + +Reduced 120G to 48G, big win (stipping files, refs, and container extra); 154203375 docs (12min to count) + +* [ ] extract not to (ident, value), but (ident, value, doc) or the like +* [ ] the joined row should contain both md blobs to generate fuller schema + +Zipped Merge + +We need: + +* refs to releases, derive key, sort +* reduced releases, derive key, sort + +* [ ] sort fatcat and refs by key +* [ ] zipped iteration over both docs (and run verify) + +---- + +# Other datasets + +* [ ] https://archive.org/details/enwiki-20210120, example: https://archive.org/download/enwiki-20210120/enwiki-20210120-pages-articles-multistream11.xml-p6899367p7054859.bz2 + +---- + +## Zipped Verification + +* beside a one blob per line model, we can run a "comm" like procedure to verify group (or run any other routine on groups) + +Advantages of zip mode: + +* only need to generate any sorted dataset; we can save the "group by" transform +* easier to carry the whole doc around, which is what we want, to generate a + more complete result document + +``` +$ skate-verify -m zip -R <(zstdcat -T0 /bigger/.cache/refcat/FatcatSortedKeys/dataset-full-date-2021-02-20.json.zst) \ + -F <(zstdcat -T0 /bigger/.cache/refcat/RefsSortedKeys/dataset-full-date-2021-02-20.json.zst) +``` + +A basic framework in Go for doing zipped iteration. + +* we need the generic (id, key, doc) format, maybe just a jq tweak + +---- + +Example size increase by carrying data to the key matching step; about 10x (3 to 30G compressed). + +---- + +* Putting pieces together: + +* 620,626,126 DOI "join" +* 23,280,469 fuzzy +* 76,382,408 pmid +* 49,479 pmcid +* 3,011,747 arxiv + +COCI/crossref has currently: + +* 759,516,507 citation links. +* we: ~723,350,228 + +``` +$ zstdcat -T0 /bigger/.cache/refcat/BiblioRefV1/dataset-full-date-2021-02-20.json.zst|LC_ALL=C wc +717435777 717462400 281422956549 +``` + +---- + +Some notes on unparsed data: + +``` + "unstructured": "S. F. Fischer and A. Laubereau, Chem. Phys. Lett. 55, 189 (1978).CHPLBC0009-2614" + +$ zstdcat -T0 /bigger/scholar/fatcat_scholar_work_fulltext.refs.json.zst| jq +-rc 'select(.biblio.title == null and .biblio.doi == null and .biblio.pmid == +null and .biblio.unstructured != null) | .biblio.unstructured' | head -1000000 +| grep -c -E ' [0-9]{1,3}-[0-9]{1,3}' +``` + +* 4400/100000; 5% of 500M would still be 25M? + + + +* pattern matching? + +``` +$ zstdcat -T0 /bigger/scholar/fatcat_scholar_work_fulltext.refs.json.zst | jq -rc 'select(.biblio.title == null and .biblio.doi == null and .biblio.pmid == null and .biblio.unstructured != null) | .biblio.unstructured' +``` + +Data lineage for "v2": + +``` +$ refcat.pyz deps BiblioRefV2 + \_ BiblioRefV2(dataset=full, date=2021-02-20) + \_ BiblioRefZippyPMID(dataset=full, date=2021-02-20) + \_ FatcatPMID(dataset=full, date=2021-02-20) + \_ ReleaseExportReduced(dataset=full, date=2021-02-20) + \_ ReleaseExportExpanded(dataset=full, date=2021-02-20) + \_ RefsPMID(dataset=full, date=2021-02-20) + \_ Refs(dataset=full, date=2021-02-20) + \_ BiblioRefFromFuzzyClusters(dataset=full, date=2021-02-20) + \_ RefsFatcatClusters(dataset=full, date=2021-02-20) + \_ RefsFatcatSortedKeys(dataset=full, date=2021-02-20) + \_ RefsReleasesMerged(dataset=full, date=2021-02-20) + \_ ReleaseExportReduced(dataset=full, date=2021-02-20) + \_ ReleaseExportExpanded(dataset=full, date=2021-02-20) + \_ RefsToRelease(dataset=full, date=2021-02-20) + \_ Refs(dataset=full, date=2021-02-20) + \_ BiblioRefZippyPMCID(dataset=full, date=2021-02-20) + \_ RefsPMCID(dataset=full, date=2021-02-20) + \_ Refs(dataset=full, date=2021-02-20) + \_ FatcatPMCID(dataset=full, date=2021-02-20) + \_ ReleaseExportReduced(dataset=full, date=2021-02-20) + \_ ReleaseExportExpanded(dataset=full, date=2021-02-20) + \_ BiblioRefZippyDOI(dataset=full, date=2021-02-20) + \_ FatcatDOI(dataset=full, date=2021-02-20) + \_ ReleaseExportReduced(dataset=full, date=2021-02-20) + \_ ReleaseExportExpanded(dataset=full, date=2021-02-20) + \_ RefsDOI(dataset=full, date=2021-02-20) + \_ Refs(dataset=full, date=2021-02-20) + \_ BiblioRefZippyArxiv(dataset=full, date=2021-02-20) + \_ RefsArxiv(dataset=full, date=2021-02-20) + \_ Refs(dataset=full, date=2021-02-20) + \_ FatcatArxiv(dataset=full, date=2021-02-20) + \_ ReleaseExportReduced(dataset=full, date=2021-02-20) + \_ ReleaseExportExpanded(dataset=full, date=2021-02-20) +``` diff --git a/python/notes/version_3.md b/python/notes/version_3.md new file mode 100644 index 0000000..8074214 --- /dev/null +++ b/python/notes/version_3.md @@ -0,0 +1,187 @@ +# 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? diff --git a/python/notes/wikipedia_citations_2020-07-14.md b/python/notes/wikipedia_citations_2020-07-14.md new file mode 100644 index 0000000..d079312 --- /dev/null +++ b/python/notes/wikipedia_citations_2020-07-14.md @@ -0,0 +1,51 @@ +# Notes on wikipedia_citations_2020-07-14 + +* https://archive.org/details/wikipedia_citations_2020-07-14 +* https://zenodo.org/record/3940692 +* https://github.com/Harshdeep1996/cite-classifications-wiki + +``` +. +├── [6.6G] citations_from_wikipedia.zip +├── [819M] lookup_data.zip +├── [1.4G] minimal_dataset.zip +├── [ 91K] wikipedia_citations_2020-07-14_archive.torrent +├── [2.0K] wikipedia_citations_2020-07-14_files.xml +├── [ 20K] wikipedia_citations_2020-07-14_meta.sqlite +└── [1.3K] wikipedia_citations_2020-07-14_meta.xml +``` + +Using `parquet-tools cat --json` +(https://stackoverflow.com/questions/36140264/inspect-parquet-from-command-line) +to convert to json. + +About 1442176 DOI, 1027006 unique. + +Most referenced on WP: + +``` + 4393 10.1073/pnas.242603899 + 3182 10.1101/gr.2596504 + 2307 10.24436/2 + 2079 10.1038/ng1285 + 1447 10.1007/BF00171763 + 1357 10.1051/0004-6361:20078357 + 1346 10.1038/nature04209 + 1293 10.1016/0378-1119(94)90802-8 + 1246 10.1016/S0378-1119(97)00411-3 + 927 10.1111/j.1096-3642.2005.00153.x + 738 10.1016/j.cell.2006.09.026 + 657 10.1101/gr.4039406 + 631 10.1101/gr.6.9.791 + 607 10.1038/msb4100134 + 602 10.1101/gr.143000 + 591 10.5194/hess-11-1633-2007 + 531 10.1101/gr.GR1547R + 492 10.1080/002229300299282 + 480 10.1101/gr.2576704 + 460 10.1093/nar/gkj139 +``` + +* https://git.archive.org/webgroup/fatcat/-/blob/10eb30251f89806cb7a0f147f427c5ea7e5f9941/proposals/2021-01-29_citation_api.md +* `source_wikipedia_article: Optional[str]` + |