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authorMartin Czygan <martin.czygan@gmail.com>2021-03-21 00:36:54 +0100
committerMartin Czygan <martin.czygan@gmail.com>2021-03-21 00:36:54 +0100
commite00e979a8b144231ce16aafe6b8482e4104f5e37 (patch)
tree942af1fbb0eeb71625438a2aaa0b1d783b84db0e /python/notes
parentc8d9268759f7da1e050658e135fac0c8f0b6fc53 (diff)
downloadrefcat-e00e979a8b144231ce16aafe6b8482e4104f5e37.tar.gz
refcat-e00e979a8b144231ce16aafe6b8482e4104f5e37.zip
initial import of python tasks
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+{"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&gt;</idno>
+ <idno>En línea] 2012 [Fecha de consulta: 21 de agosto 2015</idno>
+ <ptr target="&lt;http://dx.doi.org/10.1080/02697459.2012.661179&gt;" />
+ </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]`
+
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-21 22:03:41 +0000