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Info-PubMed

Info-PubMed. User Guide University of Tokyo, JAPAN NaCTeM, UK. Info-PubMed. (1) Info-PubMed provides information from Medline on protein-protein interactions.

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Info-PubMed

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  1. Info-PubMed User Guide University of Tokyo, JAPAN NaCTeM, UK

  2. Info-PubMed (1) Info-PubMed provides information from Medline on protein-protein interactions. (2) Given the name of a gene or protein, it shows a list of the names of other genes/proteins which co-occur in sentences from Medline, along with the frequency of co-occurrence. (3)Co-occurrence of two proteins/genes in the same sentence does not imply that they interact. Use of Information Extraction techniques allows Info-Pubmed to identify a set of sentences which clearly indicate that the interaction exists.

  3. Step 1 • Go to the InfoPubMed website https://www-tsujii.is.s.u-tokyo.ac.jp/info-pubmed/ • You will see the screen in the next slide. The red ‘Read Me’ window shows an explanation of the window that the cursor is currently in. Moving the cursor over each window will allow you to read the explanations of the ‘Trash’, ‘Interaction Viewer’, ‘Content Viewer’, ‘Gene Searcher’ and ‘My Folder’ windows. You can move a window by positioning the cursor in the coloured bar at the top of the window and pressing the left mouse button.

  4. Step 2 • In the ‘Gene Searcher’ window, enter the name of a gene or protein that you are interested in. For example, if you are interested in Raf1, type “raf1” in the ‘Gene Searcher’ and press the ‘Search’ button. You will see a list of genes whose description in our dictionary contains “raf1”.

  5. Gene/Gene Products Your are interested in Search Button

  6. Notes • The dictionary in Info-PubMed (GENIA dictionary) has 200,000 gene/protein names. • The ‘Gene Searcher’ identifies genes whose descriptions contain the given string. If the string is the name of protein, it probably appears in the field of ‘product’ in the dictionary. The field ‘product’ refers to gene products, most of which are proteins. • Other fields in a dictionary entry are ‘symbol’, ‘name’, and ‘synonym’. • By clicking the field button in the ‘Gene Searcher’ window, you can view a list of available fields and also restrict the fields that will be searched. • Boxes in the leftmost column are GeneBoxes. You can drag them to other windows, such as ‘Interaction Viewer’, ‘Content Viewer’, ‘Trash’, and ‘My Folder’. • GeneBox is indicated as “GENE” in the leftmost position in the box. The different colour indicates genes in different species.

  7. Fields By clicking this button, you can restrict search fields By clicking this button, you can restrict spieces. GeneBoxes

  8. Step 3 • Move the windows and, if necessary, adjust their sizes so that you can see the ‘Gene Searcher’ and ‘Interaction Viewer’ on your screen. • Drag one of the GeneBoxes from the ‘Gene Searcher’ to the ‘Interaction Viewer’. • to drag a GeneBox, position the cursor on the box and press the left mouse button. • You will see a list of genes/proteins which co-occur in the same sentences as the gene/proteins you moved to the window, along with co-occurrence frequency. • The GeneBox in the leftmost column is the one you have moved to ‘Interaction Viewer’. • The GeneBoxes in the second column correspond to gene/proteins which co-occur in the same sentences, followed by the boxes in the third column, InteractionBoxes.

  9. Drag this GeneBox to the Interaction Viewer

  10. The GeneBox (RAF1) you dragged intoInteractionView Genes/Proteins that interact with RAF1 InteractionBoxes

  11. Notes • An InteractionBox is indicated in the leftmost position in the box as Interaction. • In an InteractionBox, two figures are followed by the names of the two gene/protein which co-occur in the same sentences. • The first figure is the number of sentences in Medline which are judged to express direct interaction of the two gene/proteins. • The second figure is the number of sentences in which the two genes/proteins co-occur.

  12. Step 4 • Drag an InteractionBox to ‘ContentViewer’ to see the content of the box. • An InteractionBox is a set of SentenceBoxes. • A SentenceBox corresponds to a sentence in Medline in which the two gene/proteins co-occur. • A SentenceBox indicates whether the co-occurrence in the sentence is direct evidence of interaction or not. • If it is judged as direct evidence of interaction, it is indicated as Interaction. Otherwise, it is indicated as Co-occurrence.

  13. Drag this InteractionBox to ContentViewer

  14. SentenceBox Property which means the co-occurrence In the sentence is a direct evidence of interaction Property which means the co-occurrence In the sentence is a mere co-occurrence

  15. Step 5 • You can drag GeneBoxes, InteractionBoxes or SentenceBoxes to ‘My Folder’ in order to keep them for later use. • A set of programs for manipulating the boxes in ‘My Folder’, including one which draws a network based on the InteractionBoxes in ‘My Folder’, will be provided in near future..

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