add doaj subgraph notes

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+# DOAJ Citation Graph
+
+Based on Refcat (v1), the Internet Archive (IA) Scholar Citation Graph.
+
+> 2021-10-27
+
+## Basic numbers
+
+We started with a set of 4,887,241 DOI from DOAJ, after normalization we find
+4,773,245 metadata records in https://fatcat.wiki (catalog).
+
+|                                                                   | count         |
+|---------------------------------------------------------------    |-------------  |
+| matched edges                                                     | 124,760,397   |
+| matched edges (by identifier)                                     | 118,314,316   |
+| matched edges (by fuzzy matching)                                 | 6,446,081     |
+| citations **from** a DOAJ document                                | 98,616,033    |
+| citations having a DOAJ document as **target**                    | 34,910,769    |
+| citation where source and target are in DOAJ (**intra-DOAJ**)     | 8,766,405     |
+| unique source documents (all)                                     | 12,730,677    |
+| unique source documents (doaj)                                    | 3,471,878     |
+| unique target documents (all)                                     | 24,331,406    |
+| unique target documents (doaj)                                    | 2,678,972     |
+
+In words:
+
+For 72% of DOAJ documents, we have recorded at least one reference to a target
+and for 56% of the DOAJ documents, we have record at least one citation
+pointing to it.
+
+About 7% of the citation we find are intra-DOAJ, that is both the citing and
+the cited article is in DOAJ.
+
+## Charts
+
+Top referenced articles in this dataset are:
+
+| Cited By  | Fatcat Release Identifier     | Title                                                                                                                                                     |
+|---------- |----------------------------   |---------------------------------------------------------------------------------------------------------------------------------------------------------  |
+| 27043     | pedretid7rd6xknd6gsrrh3wum    | A short history ofSHELX                                                                                                                                   |
+| 26974     | hzhcy7rsoravrilgyhzohwlmai    | Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement                                                                  |
+| 22543     | fiqrt3cc5jgupls3fvroghzb4y    | Fitting Linear Mixed-Effects Models Usinglme4                                                                                                             |
+| 19735     | 4dxke54hnjh4nmsjbrrlu2o5zq    | Self-efficacy: Toward a unifying theory of behavioral change.                                                                                             |
+| 17670     | 3zmp4orkdff7tk3tc3q7hvyvay    | Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method                                                          |
+| 16186     | bdsantixljesjkofonh3oqalzq    | The Achromatic Interfero Coronagraph                                                                                                                      |
+| 8758      | jubvkngt7zflbfkwsff44fxa6q    | BEAST: Bayesian evolutionary analysis by sampling trees                                                                                                   |
+| 8713      | ztl7z2e3engvtad4l5qhldmd64    | Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries                                    |
+| 8646      | ctdiwqadirftjgu77untvwbpiu    | A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding                       |
+| 8195      | 5dcgafogfvg4tfqqhobidybpna    | Basic local alignment search tool                                                                                                                         |
+| 7741      | 27tkrqbmjrfctnhmodskvwhhqa    | RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome                                                             |
+| 7488      | fyhpfh5lkjgl7ewr7pcgrzekha    | Structure validation in chemical crystallography                                                                                                          |
+| 7266      | tdsusrfiuzcqxnnlbmm6uzyh4m    | The PRISMA Statement for Reporting Systematic Reviews and Meta-Analyses of Studies That Evaluate Health Care Interventions: Explanation and Elaboration   |
+| 7242      | qhqpojpbuvh4zffs4dvqs4beyi    | BLAST+: architecture and applications                                                                                                                     |
+| 7085      | joktmyyu5vdv3kuxm42zzqhn3e    | Hallmarks of Cancer: The Next Generation                                                                                                                  |
+| 6934      | xku5g3hmm5eangsczpzjrctd7e    | Gapped BLAST and PSI-BLAST: a new generation of protein database search programs                                                                          |
+| 6806      | srzvnzj7rvbbhig37uw6vh6m4u    | The Sequence Alignment/Map format and SAMtools                                                                                                            |
+| 6685      | tgwxkq5jnjfc3eu3zpycilq7xm    | Using thematic analysis in psychology                                                                                                                     |
+| 6554      | 5g42373tjfecxp44yqns7qwzoe    | The RAST Server: Rapid Annotations using Subsystems Technology                                                                                            |
+| 6489      | wbkhvqxm2napppgmaxin66upgm    | WGCNA: an R package for weighted correlation network analysis                                                                                             |
+| 6215      | atq75qnkkzdadbhaslevbmdlaq    | Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2                                                                           |
+| 6192      | jhoeu43y7rhoxd5eaw3dqzc4tm    | Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing                                                               |
+| 6124      | pebeuwozure4xiaygfs6om4fya    | Arlequin (version 3.0): An integrated software package for population genetics data analysis                                                              |
+| 5900      | ym7irtp4dveurpinpuyfjjdyuu    | FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments                                                                                  |
+| 5894      | dy3dpacbd5a6dag42nnsjh3pte    | Fast gapped-read alignment with Bowtie 2                                                                                                                  |
+| 5891      | nm4tov3wxndjjjpnyoqe5lirom    | MUSCLE: multiple sequence alignment with high accuracy and high throughput                                                                                |
+| 5861      | tcwbgpm3kfbnxk3lhwgsaswmrm    | Trimmomatic: a flexible trimmer for Illumina sequence data                                                                                                |
+| 5853      | j5bjclahkjfxtm6px3germagpm    | MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0                                                                                               |
+| 5818      | nttk476glncuhbuy4vvskrwfoi    | Projections of Global Mortality and Burden of Disease from 2002 to 2030                                                                                   |
+| 5644      | 7bsqead3n5he3gmbzkmfetdj3e    | MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets                                                                           |
+
+Top most referenced articles belonging to DOAJ:
+
+| Cited By  | Fatcat Release Identifier     | Title                                                                                                                                                                                                     |
+|---------- |----------------------------   |-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------    |
+| 257       | 42lwecjh4nhjbbfx5j6feoy4re    | Evidence for large domains of similarly expressed genes in the <it>Drosophila </it> genome                                                                                                                |
+| 254       | ns4v2jvhgbhh7mbg45bjtpzway    | A new natural hybrid of Iris (Iridaceae) from Chongqing, China                                                                                                                                            |
+| 220       | yqhzw62yhbd4xnfm6qkplk5gky    | Three new subterranean species of Baezia (Curculionidae, Molytinae) for the Canary Islands                                                                                                                |
+| 206       | fbr3cmn7svdyrk2de74p4ibhra    | Dwarfs of the fortress: A new cryptic species of dwarf gecko of the genus Cnemaspis Strauch, 1887 (Squamata, Gekkonidae) from Rajgad fort in the northern Western Ghats of Maharashtra, India             |
+| 187       | vwbvqztj7zbznhejreb6nmkghq    | A role for <it>cryptochromes</it> in sleep regulation                                                                                                                                                     |
+| 187       | pv7gwyji7nbh7et776cnmdok3a    | A new species of day gecko (Reptilia, Gekkonidae, Cnemaspis Strauch, 1887) from Sri Lanka with an updated ND2 gene phylogeny of Sri Lankan and Indian species                                             |
+| 164       | x3ahxq56c5bwrlf6pkmpmohqmm    | The laboratory rat: Relating its age with human′s                                                                                                                                                         |
+| 162       | 75iqitudtbcrxn73dvwv7vka5m    | On the Generalized Distance in Statistics                                                                                                                                                                 |
+| 157       | rdk724wf75ddhc5qszf53jytuy    | Immunocytochemical evidence for co-expression of Type III IP<sub>3</sub> receptor with signaling components of bitter taste transduction                                                                  |
+| 142       | dlnghkvx7bgotfftqvp5rsgeg4    | Reactivation of a silenced <it>H19</it> gene in human rhabdomyosarcoma by demethylation of DNA but not by histone hyperacetylation                                                                        |
+| 126       | evrrqdpegnhvpggmnxtdxjdnou    | Frequent Promoter Methylation of <it>CDH1, DAPK, RARB</it>, and <it>HIC1 </it>Genes in Carcinoma of Cervix Uteri: Its Relationship to Clinical Outcome                                                    |
+| 122       | p43ke27vpff6lcakjy4zchczhy    | A tandem repeats database for bacterial genomes: application to the genotyping of <it>Yersinia pestis</it> and <it>Bacillus anthracis</it>                                                                |
+| 119       | 4vipha52brfmpk5ydwb2tqbxh4    | Dividend Policy Growth and the Valuation of Shares                                                                                                                                                        |
+| 117       | oj66fyr4nncipn4rmc77px7q2y    | PGC-1alpha Deficiency Causes Multi-System Energy Metabolic Derangements: Muscle Dysfunction, Abnormal Weight Control and Hepatic Steatosis                                                                |
+| 114       | fdeqimfgg5ac7e6tqeov3lnkb4    | The molecular genetic linkage map of the model legume <it>Medicago truncatula</it>: an essential tool for comparative legume genomics and the isolation of agronomically important genes                  |
+| 112       | i4rp4yjw3bd6taihp3gkvjln2a    | Aprendendo a entrevistar: como fazer entrevistas em Ciências Sociais                                                                                                                                      |
+| 111       | ix3qnhyhovbwxiwycgcqofdrje    | Malarone treatment failure and <it>in vitro</it> confirmation of resistance of <it>Plasmodium falciparum</it> isolate from Lagos, Nigeria                                                                 |
+| 110       | yd7hojmywvexrpcoyql2bnlhyi    | OPERATIONAL EARTHQUAKE FORECASTING. State of Knowledge and Guidelines for Utilization                                                                                                                     |
+| 101       | uqjudwtgjngbtpr3ey3fog3roa    | Italian Privileges and Trade in Byzantium before the Fourth Crusade: A Reconsideration                                                                                                                    |
+| 101       | 6b6rdxf6fve6rj6pc7a7er4mfe    | Speciation and phylogeography in the cosmopolitan marine moon jelly, <it>Aurelia</it> sp                                                                                                                  |
+| 100       | njdobqruvzgabdzbifrbtfnhye    | The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs: Correction                                                |
+| 98        | dovwbef4crar5dvpbgbsnmjegu    | Antispilina ludwigi Hering, 1941 (Lepidoptera, Heliozelidae) a rare but overlooked European leaf miner of Bistorta officinalis (Polygonaceae): new records, redescription, biology and conservation       |
+| 97        | tlewnaq64zdclbzdva7vd3pjy4    | Beyond Empathy. Phenomenological Approaches to Intersubjectivity                                                                                                                                          |
+| 95        | 4xwg6e5qpnfuxmobn3ntj4beyi    | Knowledge and attitude toward COVID-19 among healthcare workers at District 2 Hospital, Ho Chi Minh City                                                                                                  |
+| 93        | 5ajqrpxqdjdzhahzkpqcqyp754    | HPLC-DAD-ESI-MSn identification of phenolic compounds in cultivated strawberries from Macedonia                                                                                                           |
+| 91        | nofyxyrfcjclhayeeymhtyaeia    | Biofilm formation by nontypeable <it>Haemophilus influenzae:</it> strain variability, outer membrane antigen expression and role of pili                                                                  |
+| 86        | tgrf2rfdjvhv3h2j55gydzjwiu    | Labiobaetis                       Novikova & Kluge in West Africa (Ephemeroptera, Baetidae), with description of a new species                                                                            |
+| 79        | z33rdxu3cnh65lbaze44nfi6cm    | Molecular phylogeny of Subtribe Artemisiinae (Asteraceae), including <it>Artemisia</it> and its allied and segregate genera                                                                               |
+| 79        | r2acgmnjlfcpjalpsaw6srcq5y    | Haplotype analysis of the PPARγ Pro12Ala and C1431T variants reveals opposing associations with body weight                                                                                               |
+
+## Glossary
+
+### Edge
+
+An edge connect a source metadata document with a target metadata document
+(from the fatcat catalog) and records a certain or highly likely citation of
+target document in source document.
+
+We also record (and display) unmatched references, that is reference
+information from a source, that has not been matched to a target yet. These are
+called "unmatched refs", sometimes.
+
+### Fatcat.wiki
+
+The catalog underlying Internet Archive Scholar
+
+### Internet Archive Scholar
+
+Search engine over 100M metadata and over 30M fulltext documents, updated in
+near real-time as new metadata and fulltext document become available in
+fatcat.
+
+### Internet Archive Scholar Citation Graph
+
+A citation graph derived from scholarly metadata and fulltext documents curated
+at the Internet Archive. Version 1 has been released in 10/2021. Futher information can be found here:
+
+* https://guide.fatcat.wiki/reference_graph.html
+* https://blog.archive.org/2021/10/19/internet-archive-releases-refcat-the-ia-scholar-index-of-over-1-3-billion-scholarly-citations/
+* https://arxiv.org/abs/2110.06595
diff --git a/notes/doaj_graph.md b/notes/doaj_graph.md
deleted file mode 100644
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--- a/notes/doaj_graph.md
+++ /dev/null
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-# DOAJ Citation Graph
-
-This dataset contains a subset of the edges of the Internet Archive (IA)
-Scholar Citation Graph (v1, 2021-07-28, named: refcat) where either the citing
-or the cited work (or both) are part of DOAJ.
-
-Basic numbers:
-
-* DOAJ DOI used for matching edges: 4,886,099
-* Catalog entries via DOI in fatcat: 4,773,245
-* We find 124,760,397 edges, of these; 98,616,033 have a source belonging to
-  DOAJ; 34,910,769 have an article in DOAJ as target; intra-DOAJ: 8,766,405
-* How do we find these edges? By id: 118,314,316;  via fuzzy matching:
-  6,446,081 (5.17%)
-
-The IA Scholar citation graph is documented in various places:
-
-* https://blog.archive.org/2021/10/19/internet-archive-releases-refcat-the-ia-scholar-index-of-over-1-3-billion-scholarly-citations/
-* https://guide.fatcat.wiki/reference_graph.html
-* https://arxiv.org/abs/2110.06595