- Email: [email protected]
Online searching of parasitology literature
Parasitology Today, vol. 4, no. I I, 1988
324 .........
Online Searching of Parasitology Literature J,E. Eyers and A.E.R. Taylor
To keep abreast of the expanding literature on parasitology is virtually a full-time job. But such full-time pursuit of source literature becomes impossible with other commitments, encouraging recourse to secondary sources such as abstracting journals, C u r r e n t Contents, and even Parasitology Today. Another approach - increasingly used since its
faltering introduction in the 1970s- involves online searching of computerized databases. Here, John Eyers and Angela Taylor review the application of such systems to parasitology. Most scientists are a w a r e o f the e n o r mous increase in the scientific literature, which a p p r o x i m a t e l y doubles e v e r y 1 0 - 1 5 years. All learned literature o v e r the past 300 years has been increasing
exponentially at t h e rate o f 6 - 7 % a year. In the biomedical field, the n u m b e r o f journals has increased f r o m a b o u t 1000 seventy years ago t o well o v e r 20 000 t o d a y ~. Parasitology is no e x c e p t i o n and,
in parLicular, specialists in areas such as molecular biology and i m m u n o l o g y publish n o t only in their o w n specialist journals (eg. Molecular and Biochemical Parasitology, Parasite Immunology) b u t also in journals d e v o t e d t o o t h e r disciplines such as Journal of Immunology o r
Infection and Immunity. T o keep abreast o f c u r r e n t research in all areas o f parasitology, scientists can no longer rely on a c o r e o f mainstream journals (Table I) b u t need t o make
Table I. Core parasitology journals scanned by selected databases
Journal
Acta Trapica 1944Adv. Parasitol. 1963Am.J. Trap. Meal. Hyg. 1952Angew. Parasitol. 1960Ann. Parasit Hum. Camp. 1923Ann. Sac. Belg. Med. Trap. 1920Ann. Trap. Med. ParasOL 1907Bull. Sac. PathoL Exot. Filiales 1908Bull WHO 1947Cab. ORSTOM 1963Clin. Exp. Immunol. 1966Exp. Parasitol. 195 I Folia Parasitol. 1954Helminthologia 1959Immunology 1958Infect Immun. 1970IntJ. Parasitol. 197 I Jpn.J. Parasitol. 195 I Jpn.J. Sanit Zool. 1950Jpn.J. Trap. Med. Hyg. 1959J. Egypt. Sac. Parasitol. 1972J. Helminthol. 1923J. Immunol. 1916J. Med. Entomol. 1964J. Parasitol. 1914J. Protozool. 1954J. Trap. Med. Hyg. 1898Meal. Vet. Entomol. 1987MoL Biachem. Parasit~L 1980Mosq. Borne Dis. Bull. 1984Nature 1869Parasite ImmunoL 1979Parasitology 1908Parasitology Research 1928Parasitology Today 1985-
Prac. HelminthoL Sac. Washington 1934Prac. Natl Acad. ScL USA 1915Protis~logica 1965SEAsianJ. Trap. Med. Public Health 1970Trans. R. Sac. Trap. Med. Hyg. 1907Trap. Geogr. Meal. 1949Trap. Med. Parasitol. 1949Vet Parasitol. 1975Zentralbl. Bakteriol. Mik~biol. Hyg. A 1887-
MEDLINE + + + + + + +
EMBASE + + + + +
BIOSIS Previews + + + + + +
Public Health & Tropical Medicine + + + + + + +
CAB + + + + + + +
SCISEARCH + + + + +
+
+
-
+
+
-
+ + + + + + + + +
+ + + + + + + +
+ + + + + + + + + + + + +
+ + + + + + + + + + + + + +
+ + + + + + + + + + + +
+ + + + + + +
+ + +
+ + +
+ + +
+ + +
+ + +
+ + +
+ + + + + + + +
+ + + + + + + + +
+ + + + + + + + +
+ + + + + + + + + + +
+ + + + + + + + +
+ + + + + + + + +
+
+
+
+
+
+
+ + + + + +
+ + + + + +
+ + + + + + +
+ + + + + + +
+ + + + + + +
+ + + + + +
~) 1988, Elsevier Science Publishers Ltd, (UK) 0165-6147/81~$02.00
Parasitology Today, vol. 4, no. I I, 1988
325
Table 2. Selected databasescoveringparasitology No. and types of sources covered 3200 journals; monographsindexed 1976-1981 only
Years covered 1966-
Abstracts available? Yes; selected
Updated Monthly
Selective indexingof over 9000 journals; also books, reviews, bibliographiesand data surveys
1969-
Yes;selected
Fortnightly
Excerpta Medica Abstract Journals 4500 journals; 3500 indexed coverto-cover. Symposia,thesesand letters selectively indexed
1974-
Yes; 60% have Fortnightly abstracts
All CAB Abstract Journalsincluding 8500 journals scannedas well as books, reports, theses,symposia, Helminthological Abstracts; patents and guides Protozc.alogical Abstracts; Review of Applied Entomology
1972-
Yes
Monthly
Cover-to-cover indexing of 4100 journals; alsoscansselected books and conference proceedings
1974-
No
Fortnightly
1200 journalsscannedas well as books, reports and conference proceedings
1984-
Database MEDLINE
Print versions Index Medicus; Index to Dental Literature; International Nursing Index
BIOSIS Previews
Biological Abstracts; Biological Abstracts/Reports, Reviews & Meetings
EMBASE
CAB
SCISEARCH
~cience Citation Index
Public Health & Tropical DiseasesBulletin;Abstracts on Hygiene & Communicable Tropical Medicine Diseases;Current AIDS Literature
efficient and regular use of the specialized indexing and abstracting journals
(Protozoological Abstracts, Helminthological Abstracts, Review of Applied Entomology, Tropical Diseases Bulletin, Abstracts on Hygiene and Communicable Diseases), together with those of a more general nature such as Biological Abstracts, Current Contents and Index Medicus. Most of the indexing journals need scan no more than a fraction of the toted number of journals available, since there is a natural 'clustering' of the literature. For example, Warren 2 has shown tha't all 10286 papers on schistosomiasis, dating back to the mid- 19th century, were contained in 1738 journals, but nearly one-third of these papers appeared in 19 journals, while half were contained in 50 of them. Despite this, some scientists are still not satisfied until they have searched all possible sources and seen every paper published in their field. However, manually scanning the abstracting journals, even only once a month, is still laborious. The less timeconsuming method of running an online search of the database equivalents of these indexing journals may be more cost-effective. Online retrieval of references from remote bibliographic databases, some of which contain millions of references, offers many advantages the most obvious of which is a speed that cannot be matched by manual searching. Also, the very wide range of databases available in the biomedical field 3-s (Table 2) offers a far greater cow-~rage of the literature than is usually available in most libraries.
The interactive nature of online searching, in which a 'dialogue' takes place between the host computer and the searcher, allows strategies to be adapted as the search progresses. Furthermore, most database vendors (hosts) will have available a number of biomedical databases that can be searched one after the other using the same search strategy, thereby increasing the coverage of available literature. Databases offer many more points of access than are available in the printed indexes, allowing subject terms or keywords to be combined together to yield the most relevant references. Other useful features include print-outs tailored to suit individual requirements, and the facility for storing search strategies in the host computer which can then be run automatically each time the database is updated. Careful strategy formulation (selection of keywords and their interrelationship) is of crucial importance to the success of any search. Some databases including MEDLINE (one of the databases produced by the US National Library of Medicine MEDLARS service) provide a thesaurus listing preferred subject headings which makes selection of keywords relatively simple. A disadvantage of online searching is its cost (Table 3), particularly when carried out by inexperienced searchers, although this may be offset by the time saved compared with manual searching. Until recently, most online searches were carried out by experienced intermediaries, such as information scientists and librarians, who are familiar with the
Yes; selected. Many Monthly with critical abstracts
structure of the individual databases as well as the command or search language required. However, some hosts such as Dialog and Bibliographic Retrieval Services (BRS) have developed, or are developing, 'end-user' programs that allow inexperienced searchers to access databases through simple menu-driven systems without the need to be conversant with command languages or database indexing systems. Microcomputers are now used in many research laboratories and, with only the addition of communications software and an inexpensive modem, they can be used to link the parasitologist directly with remote databases. Such a link could be particularly useful where no online search services are locally available. Principles of O n l i n e Searching
Online searches are initiated by telephoning remote 'host' mainframe computers on which the databases are stored. The essential equipment includes a telephone line, terminal, communications software package, modem and printer. Microcomputers, instead of the 'dumb' teletype terminal, are now universally used for online searching because they can both store and manipulate the results of searches, and can carry out word processing and data analysis. Some of the communications software packages such as 'Connect', 'Crosstalk', 'Headline' and 'Procomm' are suitable for searching bibliographical databases such as MEDLINE and BIOSIS.
326
Parasitology Today, vol. 4, no. I I, 1988
Set 1 STRONGYLOIDES
preparation of search terms is necessary for this method, because of the need to consider synonyms, singular and plural uses of words, American and English variations in spelling, and homonyms (same spelling of a word, but different meaning). There is also a tendency for greater recall or retrieval of papers with less precision or relevance. Information implicitly but not overtly included in the title or abstract may also be missed.
OR I STRONGYLOIDIASlSI
Set 2 I STRONGYLOIDES I I OR STRONGYLOIDIASlS AND (SET 1) I
I
Set 3 STRONGYLOIDES I ] STRONGYLOIDIASlS IN HUMANS NOT (SET 2)
HUMANS
I. RUSSIAN LANGUAGE PAPERS
Database Variation
SS,AN PAPERS
Fig. I. Diagram illustratJng useof Boolean operators OR, AND, NOT.Each setrepresentsa single step in the search. Shaded areas ontherightindicate aspects of the subjects required.
They cost between £120 and £300 ('Procomm' is a powerful 'shareware' package costing only US$25 registration fee). Most communications software packages offer enhancements such as the storage of passwords used to access host systems, the storage of frequently used keywords and phrases, as well as a capture facility that allows saving or 'downloading'the references on to disk. The modem, which links the telephone line and the microcomputer, converts the analogue telephone signal into a digital signal that the computer can understand, and vice versa. Modems are capable of transmitting data at various speeds such as 30 characters per second (300 Baud) and 120 characters per second (1200 Baud). Prices range from £ 120 to £700 - the faster the speed, the more expensive is the modem. Many now include communications software in the price. It is best to linkthe system to a direct telephone line rather than to one that goes through a switchboard, since switchboard operators have been known to cut in on online searches, often with expensive consequences6! Once hardware and software have been obtained, the next step is to register with one or more database hosts. A password will be issued together with manuals on how to search the system and tips on searching the individual databases on offer. Introductory training courses in online searching are also regularly held in most major cities in Europe and North America. Most systems use three basic terms to define the relationship between different subjects or concepts of the search.
These are the Boolean operators AND, OR and NOT, which are used to combine together 'sets' or groups of references on different subjects. This is best illustrated by using Venn diagrams (Fig. I ). In this example, the searcher requires references on STRONGYLOIDES or STRONGYLOIDIASIS in HUMANS, but wants to exclude all papers in RUSSIAN. Most databases use some form of indexing to arrange references on different subjects7. Some are structured so they can be searched using the same thesaurus or list of preferred terms that the indexers use at the inputting stage. Index Medicus (MEDLINE), for example, publishes its Medical Subject Headings (MESH) annually; this is arranged alphabetically by subject term, as well as in a classified alphanumeric sequence that arranges these terms in a 'genus/species' relationship (Fig. 2). The advantage of so-called controlled-language indexes is that the searcher can select the most appropriate term without having to think of synonyms, and at the same time can make use of the classified arrangement to 'explode' subjects in a particular hierarchy. As the example (Fig. 2) shows, Index Medicus lists Leishmania braziliensis, L. donovani, L. mexicana, and L. tropica under the broad term Leishmania. Thus to search papers on all species of Leishmania, it would only be necessary to enter the single term Leishmania with the appropriate 'explode' symbol. Other databases rely on natural language or the freetext approach to searching, in which the searcher enters the terms likely to be found in the title or abstract of the paper. More careful
To illustrate the way search results can vary, two simple freetext searches were carried out on the six databases outlined in Tables 2 and 3. One was for papers on Strongyloides/Strongyloidiasis and the other for papers on Cryptosporidium/ Cryptosporidiosis, both from 1984 onwards. For retrieval of the species as well as clinical aspects of both diseases, we used the roots STRONGYLOID and CRYPTOSPORIDI which also standardized the search strategy as far as possible. The wide variations in results from the six databases (Table 4) can be attributed to several factors, such as the number of sources and type of publication scanned (journal, book, or conference proceedings), and the degree to which each database producer selects items for inclusion from each source scanned (few producers input all journals 'cover-tocover'). Databases having a greater ratio of abstracts to the total number of papers will tend to perform better in terms of recall, but not necessarily in terms of precision or relevance. SCISEARCH contains no abstracts and relies mainly on keyword searching in the title. This may be no bad thing since scientific papers usually contain important keywords in the title which should result in greater relevance of papers retrieved. Incidentally, the assigning of keywords to papers by their authors at the time of submission of manuscripts for publication has little or no significance for online searching as database producers tend not to use them. Furthermore, increasing use of citation analysis in assessing academic performance makes the choice of title words, as an aid to retrieval, of crucial importance; immortality is more likely to be achieved through careful selection of keywords in titles and summaries*t Where a thesaurus exists for a database, judicious use
*Citation analysisusingSCISEARCHis increasingly used to assessthe 'qualityof academicpapers'particularlyinthe USA.
Parasitology Today, vol. 4, no. / I, 1988
327
Table 3. Selected databasehosts and costs Cost in U S $ per connect hour
Cost in U S $ per online print ref. 0.14 0.33 0.57 0.37
Cost in U S $ per offline print ref. 0.11 0.31 0.4 I 0.32
Tel: (518) 783-7251
Database MEDLINE BIOSIS Previews EMBASE CAB
DATASTAR Datastar Marketing Ltd, PlazaSuite, I 14Jermyn Street, London SWI Y 6HJ, UK. Tel: (01 ) 930-5503
MEDLINE BIOSIS Previews EMBASE SCISEARCH
20•37 76/101 73•89 1191144b
0.06 0.28 0.50 0.31
0.18 0.33 0.39 0.38
DIALOG Dialog Information Services Inc., 3460 Hillview Avenue, PaloAlto, CA 94304, USA. Tel: (415) 858-3785
MEDLINE BIOSIS Previews EMBASE CAB SCISEARCH
21136 76•93 81196 42/57 1381153b
0.05 0.32 0.55 0.30 0.41
0.20 0.40 0.42 0.35 0.41
Host
BRS Bibliographic Retrieval Services Inc., 1200 Route 7, Latham, NY 121 I 0, USA.
DIMDI Deutsches Instit~it f~JrMedizinisches Dokumentation und Information, Weisshausstrasse 27, Postfach42 05 80, D-5000 Cologne 4 I, FR Germany.
Tel: (22 I) 4724- I
minimum~maximum" 13/31 61/74 62/75 41/54
MEDLINE
20•33
0.00
BIOSIS Previews EMBASE
61/75 61/75 27•41
0.15 0.29 0.25
0.07 0.22 0.23 0.29
94/I 15b 49/70
0.23 0.50
0.27 0.54
CAB SCISEARCH Public Health & Tropical Medicine
"Figuresare basedon discountsa~Jlable for guaranteednumber of hoursof use. bThere isa reduced rate for subscribersto ISI print indexes(ell. ScienceCitation Index).
of both natural language terms and thesaurus terms can improve results, particularly when a subject is; new and its terminology is inadequately served in the thesaurus. Finally, the time-lag between journal publication and the availability of its articles online could be important, particularly if current information is needed. In addition to the results outlined above, references from a sample year (1985) of the searches were printed giving basic details - author, title and journal reference - to see how far the databases overlapped. The results were surprising. For the Strongyloides/ Strongyloidiasis search, BIIOSIS had a total of 20 unique references (out of a total of 75 papers retrieved), MEDLINE 29 (77), EMBASE 8 (54), CAB 67 (I 27), Public Health and Tropical Medicine I (17) and SCISEARCH I (20). There were 34 papers duplicated, 13 of which appeared in 3 databases, 17 in 4, 9 in 5 and 4 in all 6. In the Cryptosporidiuml Cryptosporidiosis search, BIOSIS had I I unique references (out of a total of 81
references), MEDLINE I 0 (I 97), EMBASE 8 (68), CAB 50 (132), Public Health and Tropical Medicine 4 (39) and SCISEARCH 7 (92). There were 32 papers duplicated, 31 of which appeared in 3 databases, 16 in 4, 18 in 5 and 18 in all 6. This shows, despite the small sample,
that it would be prudent not to rely on single-database searching if papers are notto be missed. Taken as a whole, this rather cursory examination of search results illustrates that caution should always be exercised in relying exclusively on online searches
TRYPANOSOMATIDAE CRITHIDIA LEISHMANIA LEISHMANIA BRAZlLIENSIS LEISHMANIA DONOVANI LEISHMANIA MEXlCANA LEISHMANIA TROPICA TRYPANOSOMA T R Y P A N O S O M A BRUCEI BRUCEI T R Y P A N O S O M A BRUCEI GAMBIENSE TRYPANOSOMA CONGOLENSE T R Y P A N O S O M A CRUZI T R Y P A N O S O M A LEWlSI
B1.841.443.868 B 1.841.443.868.110
B1.841.443.868.488 B1.841.433.868.488.80 B1.841.443.868.488.230 B 1.841.443.868.488.410 B1.841.443.868.488.680 B1.841.443.868.887 B1.841.443.868.887.80 B 1.841.443.868.887.110 B 1.841.443.868.887.128 B 1.841.443.868.887.140 B1.841.443.868.887.410
Fig. 2. An example from Index Medicus Medical SubjectHeadings (MESH) Tree Structures 1988. Online searchescan make use of classifiedsequencesto'explode' chosenclasses.The systemalso allows broader terms to be selected if required. E/ther names or numbers can be used in the search. (Reproducedby kind permiss/onof the US NatJonal Library of Medicine.)
Table 4. A comparative search of six databases
Subject
StrongyloideslStrongyloidiasis 1984-16 Aug 1988 CryptosporidiumlCryptosporidiosis 1984-16 Aug 1988
MEDLINE 385 509
No. items (abstracts, papers etc.) retrieved Public Health & BIOSIS Tropical SCISEARCHb E M B A S E Previews Medicine" CAB 173 230 360 98 473 490 347 466 227 550
"Important itemsof humanrelevanceonly are selectedfor critical abstractingby experts,thusthere are relatively few papershere. b Restrictedto title words only as!;CISEARCH hasno abstract~
328
Parasitology Today, vol. 4, no. I I, 1988
for literature searching. Scientists should take advantage of the ease and costeffectiveness of online searching, but it is only one of the weapons in the armour/ for keeping up-to-date.
N e w Databases New databases are appearing at a rate that cannot sustain the commercial survival of them all, particularly as there is an increasing tendency for databases to cover narrower, more specialized subjects. For example, there are now databases devoted to subjects such as nudeotide sequencing (Nucleotide Sequence Search System), drug sideeffects (SEDBASE) and AIDS (AIDS). The more specialized the database, the more precarious will be its commercial future, and some producers of small databases have pooled their files to produce more attractive packages. The use of compact disk technology (CD-ROM) to mount bibliographic databases is now
a rapidly expanding field, and already most of the major databases such as MEDLINE, SCISEARCH and EMBASE are available in this medium 8. CD-ROM offers most of the advantages of online searching without the worry and expense of accessing remote hosts; searches can be conducted in a more leisurely fashion with more opportunities for 'browsing'. The medium may be particularly appropriate for use in developing countries where access via satellite telecommunications to remote databases may not be available. However, costs of individual CD-ROM packages are still high, making them more suitable for institutional or library purchase. New copyright legislation is being enacted in some areas of the world which will affect downloading of references for storage and reuse in in-house databases (text retrieval software makes this practice relatively simple). Individuals who store downloaded references in their own microcomputers should seek permission from database producers -
payment is usually required. In the UK, registration under the Data Protection Act is also advisable if references are to be stored in this way.
References I de Solla Price, D. (1981) in Coping with the BiomedicalLiterature: a Primerfor the Scientist and Clinician (Warren, K.S., ed.), pp 3-16, Praeger 2 Warren, I~S.( 1981) in Copingwith the Biomedical Literature: a Primer for the Scientist and Clinician(Warren,K.S.,ed.),pp 17-30,Praeger 3 Hall,J.L.(1987)OnlineBibliographicDatabases: a DirectoryandGuide(4thedn)Aslib 4 Farbey, R. (I 987) Medical Databases 1988 Aslib S Snow,B.(1985)Database8, 15-44 6 Turpie,G. (1987)GoingOnline 1988Aslib 7 Armstrong, C.J. and Large,J.A. (eds) (1988) Manualof OnlineSearchStrategiesGower 8 Churchill, K. (ed.) (1987) The CD-ROM DirectoryTFPLPublishing John Eyers is Readers' Services Librarian at the London School of Hygiene and Tropical Medicine, Keppel Street, London WC I E 7HT, UK. Angela Taylor is with the Bureau of Hygiene and Tropical Diseases,based at the same address.
The Effect of m Mosquito Breeding Lu Bao-lin Surface agents to smother mosquito breeding sites have been used extensively for mosquito larval control. Such agents range from oil films and chemical monolayers, to expanded polystyrene beads ~'2. Here, Lu Bao-lin discusses the use 0fAzolla - a floating fern - for a similar effect. The fern has the additional advantage of providing a useful source of green manure as a crop fertilizer. Azolla is a genus of free-floating ferns, belonging to the family Azollaceae. It consists of six species - A. caroliniana, A. filiculoides, A. rnexicana, A. microphylla, A. nilotica and A. pinnata. The fern lives in association with a blue-green algal symbiont, Anabaena azolla, which fixes enough atmospheric nitrogen for rapid growth of the plant. Thus the AzollaAnabaena complex offers a source of organic fertilizer. The mineralization rate of nitrogen fixed by the AzollaAnabaena complex differs among species and strains, but it can produce up to 1000 kg of green manure per hectare per day 3 and supply 70 kg nitrogen per hectare when grown 4-6 times per rice crop. This nitrogen promotes rice yields comparable to that obtained by 70- 100 kg/ha of chemical fertilizer 4. Azolla has been used in China and other countries as a means to improve fertility of rice paddy soil and as an animal feed. In 1983,
in the Sichuan province of SW China alone, the total area in which Azolla was associated with rice cultivation exceeded 130 000 has. In the past, the question as to whether the coverage of standing water by freefloating plants, including Azolla, could be detrimental to mosquito breeding has been frequently raised 6 7' . However, no detailed study has been carried out to test this idea under experimental conditions. Recently, it was reported from
Guatemala that the aquatic fern Salvinia auriculata had a marked inhibitory effect on anopheline breeding 8. Cage tests indicated that floating vegetation could be a barrier to oviposition of gravid Anopheles albimanus. Studies of the effect of Azolla have since been reported from China, Japan and Sri Lanka9-11 . In China, laboratory studies of the effect of Azolla filiculoides on mosquito breeding have been carried out in cages under well-controlled conditions. Complete coverage of the water surface by this plant had an inhibitory effect on the oviposition of Culex tritaeniorhynchus, the principal vector of Japanese encephalitis9, Further studies under similar conditions not only confirmed the previous
Table I. The effect ofA. filiculoides on the oviposition of some culicine mosquitoes Number of egg rafts in different oviposition containers Number of Complete Mosquito species replicates coverase 2/3Coverage Control Culexmodestus I0 13 480 901 Cx paUens 7 0 64 223 Cx quinquefasciatus 8 0 105 429 Cx tritaeniorhynchus I0 I 136 201 ~) 1988, ElsevierScience Publishers Ltd, (UK) 0165-6147188/$02.00
324 .........
Online Searching of Parasitology Literature J,E. Eyers and A.E.R. Taylor
To keep abreast of the expanding literature on parasitology is virtually a full-time job. But such full-time pursuit of source literature becomes impossible with other commitments, encouraging recourse to secondary sources such as abstracting journals, C u r r e n t Contents, and even Parasitology Today. Another approach - increasingly used since its
faltering introduction in the 1970s- involves online searching of computerized databases. Here, John Eyers and Angela Taylor review the application of such systems to parasitology. Most scientists are a w a r e o f the e n o r mous increase in the scientific literature, which a p p r o x i m a t e l y doubles e v e r y 1 0 - 1 5 years. All learned literature o v e r the past 300 years has been increasing
exponentially at t h e rate o f 6 - 7 % a year. In the biomedical field, the n u m b e r o f journals has increased f r o m a b o u t 1000 seventy years ago t o well o v e r 20 000 t o d a y ~. Parasitology is no e x c e p t i o n and,
in parLicular, specialists in areas such as molecular biology and i m m u n o l o g y publish n o t only in their o w n specialist journals (eg. Molecular and Biochemical Parasitology, Parasite Immunology) b u t also in journals d e v o t e d t o o t h e r disciplines such as Journal of Immunology o r
Infection and Immunity. T o keep abreast o f c u r r e n t research in all areas o f parasitology, scientists can no longer rely on a c o r e o f mainstream journals (Table I) b u t need t o make
Table I. Core parasitology journals scanned by selected databases
Journal
Acta Trapica 1944Adv. Parasitol. 1963Am.J. Trap. Meal. Hyg. 1952Angew. Parasitol. 1960Ann. Parasit Hum. Camp. 1923Ann. Sac. Belg. Med. Trap. 1920Ann. Trap. Med. ParasOL 1907Bull. Sac. PathoL Exot. Filiales 1908Bull WHO 1947Cab. ORSTOM 1963Clin. Exp. Immunol. 1966Exp. Parasitol. 195 I Folia Parasitol. 1954Helminthologia 1959Immunology 1958Infect Immun. 1970IntJ. Parasitol. 197 I Jpn.J. Parasitol. 195 I Jpn.J. Sanit Zool. 1950Jpn.J. Trap. Med. Hyg. 1959J. Egypt. Sac. Parasitol. 1972J. Helminthol. 1923J. Immunol. 1916J. Med. Entomol. 1964J. Parasitol. 1914J. Protozool. 1954J. Trap. Med. Hyg. 1898Meal. Vet. Entomol. 1987MoL Biachem. Parasit~L 1980Mosq. Borne Dis. Bull. 1984Nature 1869Parasite ImmunoL 1979Parasitology 1908Parasitology Research 1928Parasitology Today 1985-
Prac. HelminthoL Sac. Washington 1934Prac. Natl Acad. ScL USA 1915Protis~logica 1965SEAsianJ. Trap. Med. Public Health 1970Trans. R. Sac. Trap. Med. Hyg. 1907Trap. Geogr. Meal. 1949Trap. Med. Parasitol. 1949Vet Parasitol. 1975Zentralbl. Bakteriol. Mik~biol. Hyg. A 1887-
MEDLINE + + + + + + +
EMBASE + + + + +
BIOSIS Previews + + + + + +
Public Health & Tropical Medicine + + + + + + +
CAB + + + + + + +
SCISEARCH + + + + +
+
+
-
+
+
-
+ + + + + + + + +
+ + + + + + + +
+ + + + + + + + + + + + +
+ + + + + + + + + + + + + +
+ + + + + + + + + + + +
+ + + + + + +
+ + +
+ + +
+ + +
+ + +
+ + +
+ + +
+ + + + + + + +
+ + + + + + + + +
+ + + + + + + + +
+ + + + + + + + + + +
+ + + + + + + + +
+ + + + + + + + +
+
+
+
+
+
+
+ + + + + +
+ + + + + +
+ + + + + + +
+ + + + + + +
+ + + + + + +
+ + + + + +
~) 1988, Elsevier Science Publishers Ltd, (UK) 0165-6147/81~$02.00
Parasitology Today, vol. 4, no. I I, 1988
325
Table 2. Selected databasescoveringparasitology No. and types of sources covered 3200 journals; monographsindexed 1976-1981 only
Years covered 1966-
Abstracts available? Yes; selected
Updated Monthly
Selective indexingof over 9000 journals; also books, reviews, bibliographiesand data surveys
1969-
Yes;selected
Fortnightly
Excerpta Medica Abstract Journals 4500 journals; 3500 indexed coverto-cover. Symposia,thesesand letters selectively indexed
1974-
Yes; 60% have Fortnightly abstracts
All CAB Abstract Journalsincluding 8500 journals scannedas well as books, reports, theses,symposia, Helminthological Abstracts; patents and guides Protozc.alogical Abstracts; Review of Applied Entomology
1972-
Yes
Monthly
Cover-to-cover indexing of 4100 journals; alsoscansselected books and conference proceedings
1974-
No
Fortnightly
1200 journalsscannedas well as books, reports and conference proceedings
1984-
Database MEDLINE
Print versions Index Medicus; Index to Dental Literature; International Nursing Index
BIOSIS Previews
Biological Abstracts; Biological Abstracts/Reports, Reviews & Meetings
EMBASE
CAB
SCISEARCH
~cience Citation Index
Public Health & Tropical DiseasesBulletin;Abstracts on Hygiene & Communicable Tropical Medicine Diseases;Current AIDS Literature
efficient and regular use of the specialized indexing and abstracting journals
(Protozoological Abstracts, Helminthological Abstracts, Review of Applied Entomology, Tropical Diseases Bulletin, Abstracts on Hygiene and Communicable Diseases), together with those of a more general nature such as Biological Abstracts, Current Contents and Index Medicus. Most of the indexing journals need scan no more than a fraction of the toted number of journals available, since there is a natural 'clustering' of the literature. For example, Warren 2 has shown tha't all 10286 papers on schistosomiasis, dating back to the mid- 19th century, were contained in 1738 journals, but nearly one-third of these papers appeared in 19 journals, while half were contained in 50 of them. Despite this, some scientists are still not satisfied until they have searched all possible sources and seen every paper published in their field. However, manually scanning the abstracting journals, even only once a month, is still laborious. The less timeconsuming method of running an online search of the database equivalents of these indexing journals may be more cost-effective. Online retrieval of references from remote bibliographic databases, some of which contain millions of references, offers many advantages the most obvious of which is a speed that cannot be matched by manual searching. Also, the very wide range of databases available in the biomedical field 3-s (Table 2) offers a far greater cow-~rage of the literature than is usually available in most libraries.
The interactive nature of online searching, in which a 'dialogue' takes place between the host computer and the searcher, allows strategies to be adapted as the search progresses. Furthermore, most database vendors (hosts) will have available a number of biomedical databases that can be searched one after the other using the same search strategy, thereby increasing the coverage of available literature. Databases offer many more points of access than are available in the printed indexes, allowing subject terms or keywords to be combined together to yield the most relevant references. Other useful features include print-outs tailored to suit individual requirements, and the facility for storing search strategies in the host computer which can then be run automatically each time the database is updated. Careful strategy formulation (selection of keywords and their interrelationship) is of crucial importance to the success of any search. Some databases including MEDLINE (one of the databases produced by the US National Library of Medicine MEDLARS service) provide a thesaurus listing preferred subject headings which makes selection of keywords relatively simple. A disadvantage of online searching is its cost (Table 3), particularly when carried out by inexperienced searchers, although this may be offset by the time saved compared with manual searching. Until recently, most online searches were carried out by experienced intermediaries, such as information scientists and librarians, who are familiar with the
Yes; selected. Many Monthly with critical abstracts
structure of the individual databases as well as the command or search language required. However, some hosts such as Dialog and Bibliographic Retrieval Services (BRS) have developed, or are developing, 'end-user' programs that allow inexperienced searchers to access databases through simple menu-driven systems without the need to be conversant with command languages or database indexing systems. Microcomputers are now used in many research laboratories and, with only the addition of communications software and an inexpensive modem, they can be used to link the parasitologist directly with remote databases. Such a link could be particularly useful where no online search services are locally available. Principles of O n l i n e Searching
Online searches are initiated by telephoning remote 'host' mainframe computers on which the databases are stored. The essential equipment includes a telephone line, terminal, communications software package, modem and printer. Microcomputers, instead of the 'dumb' teletype terminal, are now universally used for online searching because they can both store and manipulate the results of searches, and can carry out word processing and data analysis. Some of the communications software packages such as 'Connect', 'Crosstalk', 'Headline' and 'Procomm' are suitable for searching bibliographical databases such as MEDLINE and BIOSIS.
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Set 1 STRONGYLOIDES
preparation of search terms is necessary for this method, because of the need to consider synonyms, singular and plural uses of words, American and English variations in spelling, and homonyms (same spelling of a word, but different meaning). There is also a tendency for greater recall or retrieval of papers with less precision or relevance. Information implicitly but not overtly included in the title or abstract may also be missed.
OR I STRONGYLOIDIASlSI
Set 2 I STRONGYLOIDES I I OR STRONGYLOIDIASlS AND (SET 1) I
I
Set 3 STRONGYLOIDES I ] STRONGYLOIDIASlS IN HUMANS NOT (SET 2)
HUMANS
I. RUSSIAN LANGUAGE PAPERS
Database Variation
SS,AN PAPERS
Fig. I. Diagram illustratJng useof Boolean operators OR, AND, NOT.Each setrepresentsa single step in the search. Shaded areas ontherightindicate aspects of the subjects required.
They cost between £120 and £300 ('Procomm' is a powerful 'shareware' package costing only US$25 registration fee). Most communications software packages offer enhancements such as the storage of passwords used to access host systems, the storage of frequently used keywords and phrases, as well as a capture facility that allows saving or 'downloading'the references on to disk. The modem, which links the telephone line and the microcomputer, converts the analogue telephone signal into a digital signal that the computer can understand, and vice versa. Modems are capable of transmitting data at various speeds such as 30 characters per second (300 Baud) and 120 characters per second (1200 Baud). Prices range from £ 120 to £700 - the faster the speed, the more expensive is the modem. Many now include communications software in the price. It is best to linkthe system to a direct telephone line rather than to one that goes through a switchboard, since switchboard operators have been known to cut in on online searches, often with expensive consequences6! Once hardware and software have been obtained, the next step is to register with one or more database hosts. A password will be issued together with manuals on how to search the system and tips on searching the individual databases on offer. Introductory training courses in online searching are also regularly held in most major cities in Europe and North America. Most systems use three basic terms to define the relationship between different subjects or concepts of the search.
These are the Boolean operators AND, OR and NOT, which are used to combine together 'sets' or groups of references on different subjects. This is best illustrated by using Venn diagrams (Fig. I ). In this example, the searcher requires references on STRONGYLOIDES or STRONGYLOIDIASIS in HUMANS, but wants to exclude all papers in RUSSIAN. Most databases use some form of indexing to arrange references on different subjects7. Some are structured so they can be searched using the same thesaurus or list of preferred terms that the indexers use at the inputting stage. Index Medicus (MEDLINE), for example, publishes its Medical Subject Headings (MESH) annually; this is arranged alphabetically by subject term, as well as in a classified alphanumeric sequence that arranges these terms in a 'genus/species' relationship (Fig. 2). The advantage of so-called controlled-language indexes is that the searcher can select the most appropriate term without having to think of synonyms, and at the same time can make use of the classified arrangement to 'explode' subjects in a particular hierarchy. As the example (Fig. 2) shows, Index Medicus lists Leishmania braziliensis, L. donovani, L. mexicana, and L. tropica under the broad term Leishmania. Thus to search papers on all species of Leishmania, it would only be necessary to enter the single term Leishmania with the appropriate 'explode' symbol. Other databases rely on natural language or the freetext approach to searching, in which the searcher enters the terms likely to be found in the title or abstract of the paper. More careful
To illustrate the way search results can vary, two simple freetext searches were carried out on the six databases outlined in Tables 2 and 3. One was for papers on Strongyloides/Strongyloidiasis and the other for papers on Cryptosporidium/ Cryptosporidiosis, both from 1984 onwards. For retrieval of the species as well as clinical aspects of both diseases, we used the roots STRONGYLOID and CRYPTOSPORIDI which also standardized the search strategy as far as possible. The wide variations in results from the six databases (Table 4) can be attributed to several factors, such as the number of sources and type of publication scanned (journal, book, or conference proceedings), and the degree to which each database producer selects items for inclusion from each source scanned (few producers input all journals 'cover-tocover'). Databases having a greater ratio of abstracts to the total number of papers will tend to perform better in terms of recall, but not necessarily in terms of precision or relevance. SCISEARCH contains no abstracts and relies mainly on keyword searching in the title. This may be no bad thing since scientific papers usually contain important keywords in the title which should result in greater relevance of papers retrieved. Incidentally, the assigning of keywords to papers by their authors at the time of submission of manuscripts for publication has little or no significance for online searching as database producers tend not to use them. Furthermore, increasing use of citation analysis in assessing academic performance makes the choice of title words, as an aid to retrieval, of crucial importance; immortality is more likely to be achieved through careful selection of keywords in titles and summaries*t Where a thesaurus exists for a database, judicious use
*Citation analysisusingSCISEARCHis increasingly used to assessthe 'qualityof academicpapers'particularlyinthe USA.
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Table 3. Selected databasehosts and costs Cost in U S $ per connect hour
Cost in U S $ per online print ref. 0.14 0.33 0.57 0.37
Cost in U S $ per offline print ref. 0.11 0.31 0.4 I 0.32
Tel: (518) 783-7251
Database MEDLINE BIOSIS Previews EMBASE CAB
DATASTAR Datastar Marketing Ltd, PlazaSuite, I 14Jermyn Street, London SWI Y 6HJ, UK. Tel: (01 ) 930-5503
MEDLINE BIOSIS Previews EMBASE SCISEARCH
20•37 76/101 73•89 1191144b
0.06 0.28 0.50 0.31
0.18 0.33 0.39 0.38
DIALOG Dialog Information Services Inc., 3460 Hillview Avenue, PaloAlto, CA 94304, USA. Tel: (415) 858-3785
MEDLINE BIOSIS Previews EMBASE CAB SCISEARCH
21136 76•93 81196 42/57 1381153b
0.05 0.32 0.55 0.30 0.41
0.20 0.40 0.42 0.35 0.41
Host
BRS Bibliographic Retrieval Services Inc., 1200 Route 7, Latham, NY 121 I 0, USA.
DIMDI Deutsches Instit~it f~JrMedizinisches Dokumentation und Information, Weisshausstrasse 27, Postfach42 05 80, D-5000 Cologne 4 I, FR Germany.
Tel: (22 I) 4724- I
minimum~maximum" 13/31 61/74 62/75 41/54
MEDLINE
20•33
0.00
BIOSIS Previews EMBASE
61/75 61/75 27•41
0.15 0.29 0.25
0.07 0.22 0.23 0.29
94/I 15b 49/70
0.23 0.50
0.27 0.54
CAB SCISEARCH Public Health & Tropical Medicine
"Figuresare basedon discountsa~Jlable for guaranteednumber of hoursof use. bThere isa reduced rate for subscribersto ISI print indexes(ell. ScienceCitation Index).
of both natural language terms and thesaurus terms can improve results, particularly when a subject is; new and its terminology is inadequately served in the thesaurus. Finally, the time-lag between journal publication and the availability of its articles online could be important, particularly if current information is needed. In addition to the results outlined above, references from a sample year (1985) of the searches were printed giving basic details - author, title and journal reference - to see how far the databases overlapped. The results were surprising. For the Strongyloides/ Strongyloidiasis search, BIIOSIS had a total of 20 unique references (out of a total of 75 papers retrieved), MEDLINE 29 (77), EMBASE 8 (54), CAB 67 (I 27), Public Health and Tropical Medicine I (17) and SCISEARCH I (20). There were 34 papers duplicated, 13 of which appeared in 3 databases, 17 in 4, 9 in 5 and 4 in all 6. In the Cryptosporidiuml Cryptosporidiosis search, BIOSIS had I I unique references (out of a total of 81
references), MEDLINE I 0 (I 97), EMBASE 8 (68), CAB 50 (132), Public Health and Tropical Medicine 4 (39) and SCISEARCH 7 (92). There were 32 papers duplicated, 31 of which appeared in 3 databases, 16 in 4, 18 in 5 and 18 in all 6. This shows, despite the small sample,
that it would be prudent not to rely on single-database searching if papers are notto be missed. Taken as a whole, this rather cursory examination of search results illustrates that caution should always be exercised in relying exclusively on online searches
TRYPANOSOMATIDAE CRITHIDIA LEISHMANIA LEISHMANIA BRAZlLIENSIS LEISHMANIA DONOVANI LEISHMANIA MEXlCANA LEISHMANIA TROPICA TRYPANOSOMA T R Y P A N O S O M A BRUCEI BRUCEI T R Y P A N O S O M A BRUCEI GAMBIENSE TRYPANOSOMA CONGOLENSE T R Y P A N O S O M A CRUZI T R Y P A N O S O M A LEWlSI
B1.841.443.868 B 1.841.443.868.110
B1.841.443.868.488 B1.841.433.868.488.80 B1.841.443.868.488.230 B 1.841.443.868.488.410 B1.841.443.868.488.680 B1.841.443.868.887 B1.841.443.868.887.80 B 1.841.443.868.887.110 B 1.841.443.868.887.128 B 1.841.443.868.887.140 B1.841.443.868.887.410
Fig. 2. An example from Index Medicus Medical SubjectHeadings (MESH) Tree Structures 1988. Online searchescan make use of classifiedsequencesto'explode' chosenclasses.The systemalso allows broader terms to be selected if required. E/ther names or numbers can be used in the search. (Reproducedby kind permiss/onof the US NatJonal Library of Medicine.)
Table 4. A comparative search of six databases
Subject
StrongyloideslStrongyloidiasis 1984-16 Aug 1988 CryptosporidiumlCryptosporidiosis 1984-16 Aug 1988
MEDLINE 385 509
No. items (abstracts, papers etc.) retrieved Public Health & BIOSIS Tropical SCISEARCHb E M B A S E Previews Medicine" CAB 173 230 360 98 473 490 347 466 227 550
"Important itemsof humanrelevanceonly are selectedfor critical abstractingby experts,thusthere are relatively few papershere. b Restrictedto title words only as!;CISEARCH hasno abstract~
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for literature searching. Scientists should take advantage of the ease and costeffectiveness of online searching, but it is only one of the weapons in the armour/ for keeping up-to-date.
N e w Databases New databases are appearing at a rate that cannot sustain the commercial survival of them all, particularly as there is an increasing tendency for databases to cover narrower, more specialized subjects. For example, there are now databases devoted to subjects such as nudeotide sequencing (Nucleotide Sequence Search System), drug sideeffects (SEDBASE) and AIDS (AIDS). The more specialized the database, the more precarious will be its commercial future, and some producers of small databases have pooled their files to produce more attractive packages. The use of compact disk technology (CD-ROM) to mount bibliographic databases is now
a rapidly expanding field, and already most of the major databases such as MEDLINE, SCISEARCH and EMBASE are available in this medium 8. CD-ROM offers most of the advantages of online searching without the worry and expense of accessing remote hosts; searches can be conducted in a more leisurely fashion with more opportunities for 'browsing'. The medium may be particularly appropriate for use in developing countries where access via satellite telecommunications to remote databases may not be available. However, costs of individual CD-ROM packages are still high, making them more suitable for institutional or library purchase. New copyright legislation is being enacted in some areas of the world which will affect downloading of references for storage and reuse in in-house databases (text retrieval software makes this practice relatively simple). Individuals who store downloaded references in their own microcomputers should seek permission from database producers -
payment is usually required. In the UK, registration under the Data Protection Act is also advisable if references are to be stored in this way.
References I de Solla Price, D. (1981) in Coping with the BiomedicalLiterature: a Primerfor the Scientist and Clinician (Warren, K.S., ed.), pp 3-16, Praeger 2 Warren, I~S.( 1981) in Copingwith the Biomedical Literature: a Primer for the Scientist and Clinician(Warren,K.S.,ed.),pp 17-30,Praeger 3 Hall,J.L.(1987)OnlineBibliographicDatabases: a DirectoryandGuide(4thedn)Aslib 4 Farbey, R. (I 987) Medical Databases 1988 Aslib S Snow,B.(1985)Database8, 15-44 6 Turpie,G. (1987)GoingOnline 1988Aslib 7 Armstrong, C.J. and Large,J.A. (eds) (1988) Manualof OnlineSearchStrategiesGower 8 Churchill, K. (ed.) (1987) The CD-ROM DirectoryTFPLPublishing John Eyers is Readers' Services Librarian at the London School of Hygiene and Tropical Medicine, Keppel Street, London WC I E 7HT, UK. Angela Taylor is with the Bureau of Hygiene and Tropical Diseases,based at the same address.
The Effect of m Mosquito Breeding Lu Bao-lin Surface agents to smother mosquito breeding sites have been used extensively for mosquito larval control. Such agents range from oil films and chemical monolayers, to expanded polystyrene beads ~'2. Here, Lu Bao-lin discusses the use 0fAzolla - a floating fern - for a similar effect. The fern has the additional advantage of providing a useful source of green manure as a crop fertilizer. Azolla is a genus of free-floating ferns, belonging to the family Azollaceae. It consists of six species - A. caroliniana, A. filiculoides, A. rnexicana, A. microphylla, A. nilotica and A. pinnata. The fern lives in association with a blue-green algal symbiont, Anabaena azolla, which fixes enough atmospheric nitrogen for rapid growth of the plant. Thus the AzollaAnabaena complex offers a source of organic fertilizer. The mineralization rate of nitrogen fixed by the AzollaAnabaena complex differs among species and strains, but it can produce up to 1000 kg of green manure per hectare per day 3 and supply 70 kg nitrogen per hectare when grown 4-6 times per rice crop. This nitrogen promotes rice yields comparable to that obtained by 70- 100 kg/ha of chemical fertilizer 4. Azolla has been used in China and other countries as a means to improve fertility of rice paddy soil and as an animal feed. In 1983,
in the Sichuan province of SW China alone, the total area in which Azolla was associated with rice cultivation exceeded 130 000 has. In the past, the question as to whether the coverage of standing water by freefloating plants, including Azolla, could be detrimental to mosquito breeding has been frequently raised 6 7' . However, no detailed study has been carried out to test this idea under experimental conditions. Recently, it was reported from
Guatemala that the aquatic fern Salvinia auriculata had a marked inhibitory effect on anopheline breeding 8. Cage tests indicated that floating vegetation could be a barrier to oviposition of gravid Anopheles albimanus. Studies of the effect of Azolla have since been reported from China, Japan and Sri Lanka9-11 . In China, laboratory studies of the effect of Azolla filiculoides on mosquito breeding have been carried out in cages under well-controlled conditions. Complete coverage of the water surface by this plant had an inhibitory effect on the oviposition of Culex tritaeniorhynchus, the principal vector of Japanese encephalitis9, Further studies under similar conditions not only confirmed the previous
Table I. The effect ofA. filiculoides on the oviposition of some culicine mosquitoes Number of egg rafts in different oviposition containers Number of Complete Mosquito species replicates coverase 2/3Coverage Control Culexmodestus I0 13 480 901 Cx paUens 7 0 64 223 Cx quinquefasciatus 8 0 105 429 Cx tritaeniorhynchus I0 I 136 201 ~) 1988, ElsevierScience Publishers Ltd, (UK) 0165-6147188/$02.00