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The Cell: An Image Library-CCDB – Tutorial Part 4

Following on from the last Tutorial, we’ll now take a look at the License category and how to search using the three categories of scientific terms found in The Cell.

License

The License category is useful for selecting images when a certain use is intended. For example, if you are in the media and wanted to use an image to illustrate an article, you might choose to look only at the images in the Public Domain or which use the Creative Commons – Attribution Only License. More information on the licensing particulars can be found at http://cellimages.ascb.org/pages/license.

Scientific Terms

There are three categories of scientific terms that can be searched: ‘Biology’, ‘Imaging Methods’, and ‘Anatomy’. These scientific searches all use ontological terms for their search. Ontologies are more than simple controlled vocabularies- they also impart further understanding. For example they ‘know’ that a mitochondrion is an intracellular membrane-bounded organelle inside the cell. The use of these ontologies, in addition to allowing for greater ease of collaboration with other groups using the same ontologies, are also in place to prepare The Cell for semantic web searching.

To use these ontological terms, we have incorporated a Browse Terms button for each ontology. After browsing to the correct term, double clicking it selects it.

The image below shows how one browses to the mitochondrion:

 

TIP: To revise an advanced search after the results page is shown, do not hit the back button. This will clear the search terms. Instead, click the “Advanced” link at the top of the page under the search button and you will be taken back to your search with all your terms. This is a great time saver if you have developed a very complex search and wish to only adjust one term!

TIP: After an advanced search, copy the URL from the search results page and email it to yourself or save it in a document. Pasting that URL into the address bar of your browser and hitting enter will run the search against the library at that time. So if you return every so often you can see new search results. The ability to subscribe to your search parameters is currently in development.

Results

The results of an advanced search are presented firstly with the images matching the ontology term and, secondly, with any images which may have the search term in the text. Additionally, it should be noted that the results of the search for an ontology term will present all images with a match to any term from that node in the ontology term down the entire length of the branch. If you receive too many results simply move your search down the branch and if you don’t have enough results, move your search term up the branch!

For example:

 

 

If you search for ‘Golgi-associated vesicle’ and this does not return enough results, you may try searching on ‘Golgi apparatus part’ to expand the search results, or if searching for ‘Golgi-associated vesicle’ returns too many results- search on ‘Golgi-associate vesicle membrane’ to narrow the search results

This tutorial is the fourth in a series. What else would you like to see? Please email David Orloff at [email protected] with any questions or suggestions for other tutorials.

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