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Mahmuda Khan

Mahmuda Khan. Methodology for Pattern Discovery, Validation, and Hypothesis Development from the Annotated Biological Web. Goal. To obtain training data – sentences from the literature – to validate patterns involving triplets of Arabidopsis thaliana genes, GO terms and PO terms.

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Mahmuda Khan

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  1. Mahmuda Khan Methodology for Pattern Discovery, Validation, and Hypothesis Development from the Annotated Biological Web

  2. Goal • To obtain training data – sentences from the literature – to validate patterns involving triplets of Arabidopsis thaliana genes, GO terms and PO terms

  3. Validation of Triplets What is a triplet? - (gene, GO, PO) • Arabidopsis gene • GO: Gene Ontology- universal biological process (BP) or cellular component (CC) or molecular function (MF) • PO: Plant Ontology- plant structure

  4. Examples of Triplets - (HAP1 , pollen tube guidance, sperm cell) - (SEP1, DNA binding, carpel) - (PFS2, petal morphogenesis, stamen) - (AP1, protein binding, shoot apex) - (PHOT1, vacuole, cauline leaf)

  5. Photomorphogenesis Genes http://dbserv2.informatik.uni-leipzig.de:8080/dsggs/?analysis http://pattaran.umiacs.umd.edu

  6. Flowering Time Genes http://dbserv2.informatik.uni-leipzig.de:8080/dsggs/?analysis

  7. Photosynthesis Genes http://dbserv2.informatik.uni-leipzig.de:8080/dsggs/?analysis

  8. Example of imprints for triplets (AG, sequence- specific DNA binding transcription factor, stamen) • AGencodes a transcription factor of the MADS-box family that is expressed in stamenand carpel primordia. • The MADS-box transcription factor AGAMOUS (AG) is an important regulator of stamen and fruit identity as well as floral meristem determinacy in a number of core eudicots and monocots. • The Arabidopsis homeotic gene AGAMOUS (AG) is necessary for the specification of reproductive organs (stamens and carpels) during the early steps of flower development. • The floral homeotic C function gene AGAMOUS (AG) confers stamenand carpel identity and is involved in the regulation of floral meristem termination in Arabidopsis.

  9. Example of imprints for doublets – Padmini – please provide some examples (AG, sequence- specific DNA binding transcription factor, stamen) • AGencodes a transcription factor of the MADS-box family that is expressed in stamenand carpel primordia. • The MADS-box transcription factor AGAMOUS (AG) is an important regulator of stamen and fruit identity as well as floral meristem determinacy in a number of core eudicots and monocots. • The Arabidopsis homeotic gene AGAMOUS (AG) is necessary for the specification of reproductive organs (stamens and carpels) during the early steps of flower development. • The floral homeotic C function gene AGAMOUS (AG) confers stamenand carpel identity and is involved in the regulation of floral meristem termination in Arabidopsis.

  10. What Mahmudadid: • Read scientific articles. • Retrieved imprint sentences for about 136 triplets and doublets. • Participated in an experiment to determine the effectiveness of Manjal (automated) retrieval of the imprint sentences.

  11. Thanks for listening 

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