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Digitalization and Chemical Entity Recognition of Chemisches Zentralblatt:

Digitalization and Chemical Entity Recognition of Chemisches Zentralblatt: Unrivaled Historical Information Meets Modern Technology. M. Brändle (ETH Zürich), V. Eigner-Pitto (InfoChem GmbH). Historical Importance of Chemisches Zentralblatt. 1830 Chemisches Zentralblatt 1969.

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Digitalization and Chemical Entity Recognition of Chemisches Zentralblatt:

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  1. Digitalization and Chemical Entity Recognition of Chemisches Zentralblatt: Unrivaled Historical Information Meets Modern Technology M. Brändle (ETH Zürich), V. Eigner-Pitto (InfoChem GmbH)

  2. Historical Importance of Chemisches Zentralblatt 1830 Chemisches Zentralblatt 1969 First and oldest abstracts journal in chemistry Covers chemical literature from 1830 to 1969 Describes the „birth“ of chemistry as science (vs. alchemy) 1840 1907 Chemical Abstracts … Biggest and single abstracts source in chemistry Currently >31 million papers and patents Content 1840-1906 added retrospectively 1772 1817 Gmelin Handbook … 1771 1881 Beilstein Handbook …

  3. Chemisches Zentralblatt: Content • Covers 140 years of chemistry • About 3.6 million abstracts • journal articles • patents • 900‘000 pages (115‘000 for time period 1830-1906) • 700‘000 pages with abstracts • 200‘000 pages of indexes („Register“) • Author 1830 • Subject • alphabetic 1830 • systematic 1863 • Patent 1897 • Formula 1925 • General indexes 1883

  4. History of Chemisches Zentralblatt: Rise „Pharmaceutisches Central-Blatt“, 403 abstracts/544 pages/10 journals, weekly after 8 months. 1830 1850 Title changes to „Chemisch-Pharmaceutisches Central-Blatt“ 1856 „Chemisches Central-Blatt“ 1864 Introduction of a systematic table of contents  Classification of chemistry 1879 First patent abstracts in „kleinen Mittheilungen“ 1883 1st edition of General Index 1884 In-text images 1888 273 journals excerpted

  5. History of Chemisches Zentralblatt: Prosperity 1897 Holding passes to Deutsche Chemische Gesellschaft for DM 15‘000.Introduction of patent index. 1901 Editorial office moves from Leipzig to Berlin. CA 1919 Takes over abstracts from Angew. Chem. Split into scientific (I/III) and technical part (II/IV). 1921 Begins to cover foreign patents. 1924 CZ is reunified into one journal of abstracts. 1925 Introduction of formula index. 1929 Centennial: Richard Willstätter accentuates „timeliness, exactness, completeness“ as attributes and requirements for quality of CZ.

  6. History of Chemisches Zentralblatt: Decline Pages 1940 | 1945 WW II: Difficulties in collecting information. 1944 bombing of editorial office. Editorial Office East Berlin Double production of CZ in Eastand West Germany. 1947 | 1949 1950 Reunification of CZ under Eastand West German organisations. 1954 Trying to fill gap by supplement volumes. 1961 Berlin Wall does not hinder production. 1967 Introduction of SRD (Schnellreferatedienst, quick abstract service) for organic chemistry. Editorial Office West Berlin GDR office declares unable to afford production of SRD and of journal. CZ ceases publication. 1969 CA SRD continued as „Chemischer Informationsdienst“ (ChemInform).

  7. Chemisches Zentralblatt vs. CA: Quantity Abstracts Pages WW II WW II WW I WW I CA format change

  8. Chemisches Zentralblatt vs. CA: Quality • Many textbooks on chemical literature claim better quality of Chemisches Zentralblatt than CA for pre-WW II • H. Skolnik, The literature matrix of chemistry, 1982: „outstanding A/I service“ • R.E. Maizell, How to find chemical information, 3rd ed. 1998, citing E.J. Crane, „[..] has value because of [..] good abstracts“ • M. Mücke, Die chemische Literatur, 1982, „Zwar war CA zahlenmässig [..] dem Chemischen Zentralblatt überlegen, doch war dies gerade umgekehrt, was die Qualität der Referate betraf.“ • R.T. Bottle, J.F. Rowland, Information Sources in Chemistry, 4th ed. 1993, „Before WW II, many chemists regarded CZ as superior in coverage to CA; its abstracts were longer and more informative [...]“ • A.S.K. Atsu, Comparative coverage of chemical abstracting services in the period 1906-1940, M. Sc. Thesis, City University, London (1976)

  9. Chemisches Zentralblatt vs. CA: Quality Example: Hans Fischer, Georg Stangler, Synthese des Mesoporphyrings, Mesohämins und über die Konstitution des Hämins, Justus Liebigs Ann. Chem. 459(1927), 53-98.

  10. Chemisches Zentralblatt: Digitalization • Relevant for documentation of prior art • Continuous and growing demand of the information • FIZ Chemie Berlin has scanned the whole work and offers a full text searchable database for the web and the dataset for integration in Intranets • ETH Zurich has bought the digitalized raw material (pdfs with OCRed text in the background) from FIZ and is creating a database offering full text search • 900‘000 pdf pages,1.3 TB • Raw text content incl. search index about 10 GB • CAS has performed automatic translation (German  English) of the 1897-1907 volumes and included in CAplus

  11. Reasons for buying digitalized Chem. Zentralblatt www.infochembio.ethz.ch/en/holdings.html

  12. Reasons for buying digitalized Chem. Zentralblatt • Space • Loss of compact shelving space in basement (432 m  194 m, -55%) • Disposal of printed Beilstein, CA, Chem. Zentralblatt • Access • e-books, e-journals, end-user databases at workbench of chemist • Chemists trained to electronic sources, print and µ-film cumbersome • Restoration costs due to deterioration of acid-containing paper • 17K€/t for deacidification : Chem. Zentralblatt 1.6 t  27K€ • Digitalization and operation costs much higher (10x), but can be divided • Ease of use : Search / Browse / Print

  13. Quality of Obtained Raw Data • Errors upon conversion • Visual inspection of pages: Cover Flow / Quick Look technology

  14. Quality of Raw Data Observed: Page Errors • File errors (conversion) • Unreadable directories (missing content) • Defect pdf files (missing content) • Errors during scanning (visual inpection) • Duplicate pages (shifting page index) • Missing pages (shifting page index, missing content) • Issues scanned in wrong order (minor) • Two pages on one (shifting page index) • Wrong volume (missing content)

  15. Quality of Raw Data Observed: OCR • ETH works with OCR from FIZ Chemie • page  word index, 346 million „words“ • 8.8% with only 1 character • slightly expanded fonts, e.g. for author names, sum formulas • Abbreviations (journal names, Zentralblatt = C), numbers • element names in structure formulas

  16. Planned Tasks ETH Zürich • Adding navigation structure, provide DB search and browse for ETH members (Q4/09) • Mining and Markup (Q1/10) • Bibliographic references • Authors • General Subject Headings • Reference linking to journal articles and patents (Q1/10)

  17. Chemisches Zentralblatt: Conclusion • Covers chemical literature from 1830 to 1969 • Very good abstract quality • Better quality (length, details) than CA for pre-WW II period 1907-1940 • Contains also important patent information • Invaluable information in indexes (e.g. synonyms of ancient chemical names) • Only comprehensive abstract journal on the market up to 1907 • More comprehensive than CA for 19th century literature • Complements Beilstein and Gmelin handbooks for 19th century literature

  18. Importance of Chemisches Zentralblatt: Example Org. Lett., 2006, 8 (19), pp 4279–4281 The authors have retracted this paper on November 15, 2007 (Org. Lett. 2007, 24, 5139) Chemisches Zentralblatt., 1904, 2, 1145

  19. InfoChem Motivation • Text search in Chemisches Zentralblatt: • Abstracts in German language • High number of old German chemical names • Chemists think in structures!!! • Language independent structure search would help ALL scientists to access this historical source and to use the relevant information of this art • Required technology for structure search projects • Optimized German-English dictionaries • 30 million SPRESI names

  20. Overview of Approach and Applied Technology OCR SPRESI Dictionaries Comparison (quantitative) NER N2S Manual abstraction of sample set for evaluation ICANNOTATOR .tiff Documents Database skhflaskjlkfjlkdj Combined search on federated search system (ICFEDSEARCH) Link to original literature Pdf documents Text under image

  21. Challenges OCR (1) 1830 1969 1870 1910 1930

  22. Challenges OCR (2) • Bad quality of original source: dirty (blotted, stained) pages • print from back page

  23. Challenges OCR (3) • Tables: extremely small fonts, • not recognizable begin / end of columns

  24. Challenges OCR (4) • Ambiguous old fonts (h=b; c=e; ligations) • Spaced text Specific rules, large German dictionaries and extensive training are applied to correct systematic mistakes of standard OCR process

  25. Challenges Annotation (1) • Names lack position, valence or stoichiometric information • Pimarsäure  is it the R or L form? • Platinchlorid  in which oxidation state II, III, IV? • Chemical names that indicate a chemical class • Nitrolsäure (nitrolic acid)  • Lactonsäure (lactonic acid)  any of several acids with a lactone ring bearing the carboxylic group • Mixed compounds • Eunole  Naphthole + Eucalyptusöl • Pikrotoxin  Pikrotoxinin + Pikrotin NO solution: correct structure information is not available in the original source

  26. Challenges Annotation (2) • Obsolete German language • Schwefelsaures Natrium, Chlorür, Bromür • Historical names • Pelopeum  Columbium  Niobium • Different spelling for the same name: • Dibrom…  Bibrom… • Ätzkali  Aetzkali • 

  27. Solutions in Annotation Process • Correction of German-specific grammar • Translation in English of not available chemical names • Research in old sources: • Beilstein • Brockhaus Encyclopedia • German-English dictionaries of chemistry • Meyers Encyclopedia • Pierer Encyclopedia • References to very old books, journals, articles • “Naturwissenschaftliche Exzerpte und Notizen Mitte 1877 bis Anfang 1883” • by Karl Marx

  28. Results Annotation Chemisches Zentralblatt • 120,000 pages covering time period 1830-1907 • 2.4 million chemical names with associated structure • 98,000 unique names • 47,000 unique structures Quantitative comparison with manually abstracted sample set • Recall 51% • Precision 87%

  29. Federated Search Prototype

  30. Federated Search Prototype

  31. Federated Search Prototype

  32. Summary • Described history, content and importance nowadays of Chemisches Zentralblatt • Illustrated how the challenges of OCR and annotation process have been solved • Time period 1830-1907 contains 98,000 unique names and 47,000 unique structures • Quantitative comparison proves over 50% recall and nearly 90% precision • Generated structure searchable Chemisches Zentralblatt database is integrated in ICFEDSEARCH

  33. Outlook

  34. Acknowledgements • Prof. Dr. Deplanque, Mr. Heineke and FIZ Chemie Team Berlin • Ms. Langanke • InfoChem Team • Chemistry Biology Pharmacy Information Center (ETH Zürich) Thank you! ETH Zürich: www.infochembio.ethz.ch, braendle@chem.ethz.ch InfoChem GmbH: www.infochem.de, www.spresi.com, info@infochem.de

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