PAGE and Curation Tutorial

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PAGE Search by Term Tutorial

PAGE Curation Tutorial

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Search Expression by Term

Find transcripts that are expressed in an anatomical structure using PAGE search

Search Expression by Transcript

Find anatomical structures that express your transcript using PAGE search

Search Expression by Publication

Find a manuscript’s transcripts and the structures they are expressed in using PAGE search

Search the Literature

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Add Your Data to PAGE

PAGE Search By Anatomical Term

Head to the PAGE search

  1. We STRONGLY suggest reading the About this Search, and Search tips sections at the top of each search before you get started. Below you can find the About Anatomical Term Search and Tips section to click and read, you can also find these on each search page. Because PAGE is built with the Planarian Anatomy Ontology (PLANA), there’s some relationship rules in PLANA that you’ll need to know to get expected search returns. Also consider watching the tutorial video under the About This Search Section.

    Search expression patterns in the literature using PAGE.

    PAGE is a database of published transcripts and expression patterns.

    All data were manually curated from planarian manuscripts published between 2005-2019.

    Locations of expression were collected from 200 publications.

    Locations are all standardized terms that are defined in the Planarian Anatomy (PLANA) Ontology.

    Use a location (anatomical term) to retrieve transcripts that are expressed in this location.

    The search can be modified to include other structures that are of the same type (is a) or only anatomical structures that are part of, contained in, or develops from your search term.

    In order to better understand the anatomical terms returned in your search you can browse the ontology here on Planosphere or at EBI OLS.

    Read more about PAGE

    PAGE Query by Term Video Tutorial

    Find more video tutorial help on our tutorials page.

    Searching by anatomical term will only return transcripts that were annotated as being expressed in that specific anatomical term by the authors of the evidence. This search WILL NOT return expression annotation of all equivalent transcripts from other transcriptomes. If you are interested in equivalent transcripts, use Rosetta Stone Transcript Mapper to determine them and then run independent search by transcripts to determine anatomical terms associated with the equivalent transcripts.

    General search tips:
    • Start simple. Start with just an anatomical term in the first autocomplete text box. See what is returned.
    • Try adding additional filters one at a time. Each filter can potentially reduce the number of results that are returned.
    • Since the Planarian Anatomy Ontology is not yet complete and the publications annotated in the PAGE database is finite not all searches will return results. This is where you can help PLANA and PAGE grow and become more comprehensive. Visit About PLANA to see how to contribute.
    • If you are still having issues with your search not returning results you expect it is likely due to one the points below.

    Using part of vs contained in:
    • If you search using 'head region' and part of you will get ZERO results
    • If you search using 'head region' and contained in you will get >20,000 results
    • contained in describes anatomical structures that are found within an area, such as the 'head region', 'tail region', 'midline', and, 'dorsal region'. (e.g. 'eye' contained in 'head region')
    • part of describes anatomical structures that are found within a larger anatomical structure, such as cell is part of a tissue. (e.g. 'photoreceptor neuron' part of 'eye')
    • contained in. Anatomical structures can only be contained in an 'anatomical region'
      • 'midline'
      • 'head region'
      • 'tail region'
      • 'tail tip'
      • 'tail stripe'
      • 'prepharyngeal region'
      • 'parapharyngeal region'
      • 'postpharyngeal region'
      • 'anterior tip'
      • 'anterior pole'
      • 'posterior pole'
      • 'copulatory region'

    Examples using part of
    • 'gut' part of 'digestive system'
    • 'intestinal phagocyte' part of 'gut'
    Examples using contained in
    • 'pharynx' contained in 'parapharyngeal region'
    • 'cephalic ganglia' contained in 'head region'
    • 'mouth' contained in 'ventral region'

    Other Search Examples:

    Identify transcripts associated with:

    • any anatomical term that is a ...
      • is a neoblast → will return transcripts expressed in 'zeta-neoblasts', 'sigma-neoblast', 'gamma neoblast', etc.
      • is a cephalic ganglia → will return transcripts expressed in the 'cephalic ganglia'
      • is a nervous system → will return transcripts expressed in the 'central nervous system', 'peripheral nervous system' and 'nervous system'
    • anatomical term(s) that are exactly curated as being expressed in ...
      • exactly neoblast → will return transcripts associated with 'neoblast'
      • exactly head region → will return transcripts annotated as being expressed in the 'head region'
      • exactly nervous system → will return transcripts annotated as being expressed in the 'nervous system'
    • any anatomical term that is part of ...
      • part of central nervous system → will return transcripts expressed in 'cephalic ganglia' , 'glial cell', 'optic chiasm', etc
      • part of pharynx → will return transcripts expressed in 'esophagus' , 'pharynx musculature', 'pharynx nerve plexus', etc
    • any anatomical term that is contained in ...
      • contained in the posterior region of the whole animal → will return transcripts expressed in 'tail region' , 'tail strip', 'gut', etc
      • contained in the head region → will return transcripts expressed in the 'eye' , 'cephalic ganglia', 'pigment cup cell', etc
    • any anatomical term that develops from ...
      • develops from a zeta-neoblast → will return transcripts expressed 'Category 2 cell'.
      • develops from a blastomere →will return transcripts expressed in the 'germline stem cell', 'oogonial stem cell', etc.

  2. Start simple, run a default search (don’t click any boxes under the search field), which will return transcripts that were annotated (described by the paper authors) as being expressed in that anatomical term. Start by typing your term of choice into the search field. An auto complete dropdown of PLANA terms will pop up, select the term you are interested in. YOU MUST USE A TERM FROM THE DROP DOWN THAT IS IN THE PLANA ONTOLOGY for the search to run.
  3. Let’s start with “eye”. This runs a search for all transcripts that have been recorded as being expressed exactly in the “eye”. As of September 2021, you should get 75 results (click image to zoom):
  4. The PLANA ontology organizes anatomical structures by relationship and we know that there are structures that are part of the eye. Let’s run a search to capture transcripts expressed in structures that are part of the eye. Type “eye” in the box and then click “Perform expanded search with relationships” box. Select “part of” in the drop down box that appears ABOVE the search box (to create a human readable sentence). Run the search. As of September 2021 you should get 199 results including photoreceptor neurons, optic cup, eye cell, etc.
  5. In the expanded search with relationships we can broaden the search even further to all transcripts expressed in structures that are contained in the head region. Please note there is a difference between part of and contained in relationships. Part of denotes cell:tissue:organ:system relationships while contained in is for large regions ( head, anterior, tail etc). If you run an expanded search for contained in “head region” , as of September 2021 you will get 36,197 instances of expression.

  6. If you limit the above search for experimental details (second check box) and select, whole organism, asexual adult and, insitu hybridization evidence (will include colorimetric and fluorescent), as of September 2021 you will get 3216 instances of expression.
  8. If your search is not returning expected results, please revisit the documentation at the top of each PAGE search form. You may be choosing the wrong relationship for your search. For example, searching for expression in the "head region" using the "part of" relationship will yield ZERO results because "contained in" is the proper relationship for regions. A note on expectations: PAGE is annotated using author’s language and for multiple reasons underrepresents the body of expression data in existence. For more about the limitations see the underlying curation rules.

Curate a paper for integration into PAGE

If you have already been through the tutorial, directly access the GitHub Issue Page, and the annotator

  1. Access the paper and open the annotator you will see this menu
  2. Read the annotation rules
  3. Record all instances of expression associated with only HOMEOSTATIC expression by transcript ID using the annotator.
  4. Once an expression observation has been recorded, click "Add Row". Now the observation is recorded and will be displayed to the right.
  5. When all instances of homeostatic expression are recorded for a pubmed id, download the text file from the annotator and head to the PAGE GitHub issue tracker
  6. Be sure to include PMID in the title, curation type (New, Existing, etc), and your ORCID. Most importantly, drag and drop the annotator downloaded table at the bottom. Finally, click Submit.
  7. Please keep the annotation file for your records, if we have any questions we will reach out to you to resolve.

PAGE Curation Issues Tutorial

Is the PAGE Search not returning what you expected? Are results from your publication missing or miss-annotated? Please let us know!!! We want our curations to be as correct as possible. The best way to let us know is with our GitHub issue tracker. This way everyone will know about the issues and we are held accountable.

All of this is handled in the PAGE GitHub Repository. This is the place were we share our code and data and where we handle requests and issues.

  1. You can visit the Issue Tracker directly or navigate to it with the menus in the repository. When you want to create a "New Issue" you will need to select the type of issue you would like to create. Is it about a bug in the search or webpages? A new feature request? General questions or comments? A request to curate a new paper? Or do you want to submit your own curations?
  2. To view all open issues click on the Issues link in the top menu of the repository.

    Here are all open issues.
  3. To create a new issue, click "New Issue" from the Open Issues View, and select a new issue type.
  4. Once you select an issue type. Be sure to read the text carefully and include all requested information so that can properly address your issue. Below is the form for requesting the curation of a specific publication. This form requires the Pubmed ID and any additional comments about this paper.
  5. For more information about "Submit gene expression observation curation" see the above tutorial on PAGE Curation