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Fungal databases: what are Indian scientists looking for? Shubhada Nagarkar Bioinformatics center University of Pune, India shubha@bioinfo.ernet.in Background of the study India has a rich and varied heritage of biodiversity There are databases on indigenous and medicinal plants

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fungal databases what are indian scientists looking for

Fungal databases: what are Indian scientists looking for?

Shubhada Nagarkar

Bioinformatics center

University of Pune, India

shubha@bioinfo.ernet.in

background of the study
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
poster presentation
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
slide4

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
biodiversity databases what needs to be done before database construction
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?
objectives of this study
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.
scope of the study
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
data collection through survey
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
other data collection methods
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
research methods for data collection
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.

research paper construction
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
ask gandhe mam pop up title for this field standardization for easy retrieval
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
slide13

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

use of the database
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
contents of the database at level i
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

slide16

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

slide17

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

slide18

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

slide19

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
slide20

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

for scientists involved in specimen listing classification and identification

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

for scientists involved in producing molecular sequences and bioinformatics
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
user templates
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
user template a sample based on analysis of level i and ii
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
database testing
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.
www site
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
lessons from library and information science field
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”
conclusion
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.
acknowledgements
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