Fungal databases: what are Indian scientists looking for?

1. Fungal databases: what are Indian scientists looking for? Shubhada Nagarkar Bioinformatics center University of Pune, India shubha@bioinfo.ernet.in

2. Background of the study • India has a rich and varied heritage of biodiversity • There are databases on indigenous and medicinal plants • The Indian sub-continent is characterized by diverse topography and climatic conditions. Correspondingly the sub-continent is adorned with immense fungal diversity • There are very few initiatives for documentation of fungal species • The current study is a collaborative effort of mycologists, computer professionals and library science professionals

3. Poster Presentation • Presentation is divided into three parts • Survey of information needs of mycologists • Data collection methods • Data analysis • Categorization of information based on analysis of information needs

4. Biodiversity Databases Information Retrieval Problems • Lack of user surveys • Too complex for average users and scientists • Databases are developed either by computer scientists (who are computer savvy) or biodiversity scientists (who are data savvy) – but rarely by both • Lack of metadata – data documentation

5. Biodiversity Databases what needs to be done before database construction It is necessary to find out • How research workers and students approach the topic? • How they use information artifacts (documents, images, maps, existing databases etc.) to do their work? • How they collect data? • What are the data management practices?

6. Objectives of this study • To understand the information needs of scientists involved in mycological research • To develop a database prototype to meet users’ information needs • To check compatibility of this prototype with international data standards • To test the database design with different fungal species.

7. Scope of the study • Study is limited at taxonomic level which helps in identification process of species • Survey of Information needs is restricted to • Scientists – M.Sc. / Ph.D. students, Research fellows, etc. • Farmers – innovative and traditional

8. Data collection through survey A questionnaire was circulated among 40 scientists and 10 farmers • The 40 questionnaires were analyzed according to the main research activities of the scientists which were found to be • Maintaining herbaria • Specimen listing, classification and identification • Producing molecular sequences and Bioinformatics • Farmers’ questionnaire is yet to be tested

9. Other data collection methods • Focus group study • Three focus group studies were done in three different laboratories in the city of Pune. The discussions were on • Types of information that they look for in a database • The difficulties that they faced in collecting information • What were their expectations from the database prototype • Document resources • Print and online resources : content synthesizing

10. Research Methods for data collection Interviews of defined user group to understand the difficulties they face during the data collection • Focus group study – scientists, students-M.Sc. / research, industrialists, agriculturists, farmers • Questionnaire • Survey and analysis of available online fungal databases • Survey of the contents of textbooks, reference books and research journals to understand the coverage of topics included. • Thesaurus, ontologies, dictionaries, etc. Data collected through questionnaire helps in understanding user information needs, what kind of data they need from any database. Index of Biological abstract, Medical subject heading, Agri-Index, etc. Study the structure of available online databases for eg. databases developed by various mycological societies, universities, etc. Book contents help in understanding the flow of information. Contents are helping in organizing the different topics.

11. Research paper construction When a scientist writes a research paper he/she is expected to give the following details for easy retrieval by others • Title • Authors name and address • Abstract • Keywords • Introduction • Material method • Observations • Results and discussions • Bibliography

12. Ask gandhe mam (pop up) title for this field standardization for easy retrieval • Scientists when publishing a new species cover • following information in their research paper: • Name of fungus, host, nature of fungus, • classification of fungi • Field notes • Geographical information, • Host plant information • Symptoms • Habitat / substrate of fungus • Characteristics of fungus • soral morphology • spore data • images • references

13. Research Method • Study of information • needs • Questionnaire • Interviews • Observations, etc. • Users • Students • Agriculturists • Industrialists • Pharmacists, LIS Contribution User Feedback Experts: Mycologists and Taxonomists Revised Database + Ontologies, Controlled vocabulary Database prototype and metadata Interface design, Error reports Laboratory study of revised database User behaviour (LIS contribution) Testing of initial prototype

14. Use of the database • This database can be used at two levels • Participatory resource where scientists can put in their data into this database. • Metadata will include details about the copy right/ownership of the data and other details • Shared resource where all scientists, industrialists and agriculturists can use this database for their work

15. Contents of the database at level I • Name of the fungus • Name of the host • Family of fungus • Date of collection • Collector/collected by • Field notes • Country • State, district, local area • Nature of infection • Period of infection • Effect of infection • Life cycle pattern • Types of spores • Prominent spore type • Soral morphology • Nature of sorus • Spore morphology • Bibliographic details • Images • Prevention As per the conducted survey it was found that these were the basic fields required by all scientists and agriculturists and therefore they are at level I of the database

16. Details of the fields at level I Nomenclature and taxonomic table Accession number Family Genus Species Vernacular names Geographical locations/maps Country State District, city, local area Host parasite relationship Name of the fungus Name of the host Nature of infection Period of infection Effect of infection Nature of life cycle pattern Disease symptoms Period of infection Action on host plant Path of infection General information Accession number Data of collection Collected by Field observations Soil type Ph Other field information

17. Details of the fields at level I • Spore data • Name of fungus • Types of spores • Prominent spore type • Soral morphology • Nature of sorus • Spore morphology • Structure • Size • Shape • Color • Ornamentation • Dormancy period • Number of germ pores • Spore germination • Germination pattern Images Metadata Images of individual stage Publication data Original reference Literature citation Further studies on the fungus Prevention Fungicides Resistant varieties

18. Details of the fields at level I Biochemistry of fungus Primary metabolites Secondary metabolites Products Images Metadata Images of individual stage Sequence data Protein and nucleic acid sequences Before and after infection Protein level at different time period Protein markers Publication data Original reference Literature citation Further studies on the fungus Disease management Control of fungi Application of fungicides Timings of applications Name of fungicide Dosage Resistant variety Prevention Fungicides Resistant varieties

19. Contents of the database at level II • In the same survey it was found that there were some differences in the information required by various groups of scientists who were involved in different activities like maintaining herbaria, specimen listing, classification and identification, producing molecular sequence and Bioinformatics. • Hence these fields were taken at level II of the database

20. Details of the fields at level II For scientists involved in Maintaining Herbaria Testing and screening of varieties against diseases Recent reference and recent systematic position Mode of nutritionpoisonous / non poisonousclimatic conditionforest typeh-p relationship - obligate parasite / facultativespore data - pathogenic / non pathogenic Latitude, longitude, altitude Geographical extent

21. Details of the fields at level II For scientists involved in Specimen listing, classification and identification Secondary metabolitesRecent reference and recent systematic positionMode of nutritionpoisonous / non poisonousclimatic conditionforest typeh-p relationship - obligate parasite / facultativespore data - pathogenic / non pathogenicLatitude, longitude, altitudeoospores - eccentric centric subcentria, size and numberoogonia : ornamentation, shape, size etc. Anteridial attachment to oogoniaInsect as host Host defense mechanisms, virulence factorsGeographical extentCulture - production of metabolites, / toxin, growth characteristics, optimum media for growth - ph, temperature, aeration, agitation, etc.reproductive organs- sexual and asexual

22. For scientists involved in producing molecular sequences and bioinformatics Details of the fields at level II • secondary metabolites • life cycle pattern in detail • Recent reference and recent systematic position • latitude, longitude, altitude

23. User templates • User templates were made based on information requirement at level I and level II • There were further analyzed based on the subject expertise of the mycologists • Biotechnology • Plant pathology • Microbiology • Curators

24. User template:a sample (based on analysis of level I and II) Biochemistry and biotechnology Nomenclature and taxonomy Host parasite interaction Name of host Nature of infection Effect of infection Name of disease Nature of life cycle pattern Morphology of fungus somatic structure reproductive structures Biochemistry of fungus Primary metabolites (sugar, proteins, tanin, steroids, general alkaloids) Secondary metabolites Products (antibiotics, vitamins, etc.) Disease management Curators • Name of fungus, host, nature of fungus, classification of fungi • Field notes • Geographical information, • Host plant information • Symptoms • Habitat / substrate of fungus • Characteristics of fungus • soral morphology • spore data • images • references

25. Database testing • The database will be tested at two levels • Data entry level • Data retrieval level • Once the database is tested and finalized it will be put on the world wide web.

26. WWW site Architecture • Relational database system • Several tables • Template for each type of user • Connectivity between templates User • Registration of user as per field of specialization • Retrieval of data according to templates • Database will also be in the regional language Marathi for farmers in this region. Other regional languages also be included at a later stage

27. Lessons from Library and Information Science field • The LIS tradition of conducting user surveys, finding user needs, cataloguing and classification methods are being applied in the creation of the present database on Indian fungi. • The case study of the creation of an Indian fungal species database underlines the importance of finding out about user information needs, database construction, database search skills in order to create “request oriented database”

28. Conclusion • Library and Information Science research suggests ways of providing optimal flexibility in data handling and the generation of robust, realistic standards. • Key to this is the need to study the users’ information practices in detail. • By providing for a constant feedback loop between the various user communities and the designers, we can: • Provide appropriate windows into the database for different users • Provide cautions about uncertainty in the data tailored to different user communities • Work out ways to involve different user communities in cleaning and expanding the database, and work out appropriate checks on each community’s input.

29. Acknowledgements • Prof. Harsha Parekh, SHPT school of library science, Mumbai • Dr. Kanchanganga Gandhe, Modern College, Pune, India • Prof. Geoffrey Bowker, ………. • Bioinformatics Center, University of Pune