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_at_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?

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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.

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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

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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

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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

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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.
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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

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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

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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
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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

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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

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
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Details of the fields at level I
Nomenclature and taxonomic table Accession
number Family Genus Species Vernacular names
Geographical locations/maps Country State Distric
t, 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
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Details of the fields at level I
Images Metadata Images of individual stage
Spore data Name of fungus Types of
spores Prominent spore type Soral
morphology Nature of sorus Spore
morphology Structure Size Shape Color Ornamentat
ion Dormancy period Number of germ pores Spore
germination Germination pattern
Publication data Original reference Literature
citation Further studies on the fungus
Prevention Fungicides Resistant varieties
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Details of the fields at level I
Biochemistry of fungus Primary metabolites Seconda
ry 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
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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

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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

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For scientists involved in Specimen listing,
classification and identification
Details of the fields at level II
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
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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

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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

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User templatea sample (based on analysis of
level I and II)

• 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

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
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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.

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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

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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

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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
  communitys input.

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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