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Bioseek consists of three main modules:Research, Shop,andLab.For now we focus onResearch,as the other two are still under heavy development. This video shows you the very basic navigation -the Application Switch.
Research Main menu
The Research module is your assistant in your daily work process.
The Right Panel is available throughout the entire application. It has four tabs:
It can beexpandedandcollapsedaccording to your need.
* If you navigate to a section of BioSeek which is still under heavy development, you will see the image shown below. We are working hard to bring this functionality to you ASAP
Search by tags, Dynamic search suggestions, Shortcuts
To get started with your searches on Bioseek, go to module“Research”,tab“Search”
To unlock the full potential of BioSeek you usetagsinstead of wordsto search.The links between the different entities are best analyzed when tags are used. Each entity has a pertaining tag to search it by.
Why use Tags instead of text?
More accurate results;
Tags are drag-droppable;
Flexible - tags have priority levels.
Entities, indexed as tags by Bioseek, are:
Let’s create some tags and see how BioSeek works.
Go to Research > Search
Click Search Box
Select the correct tag from the suggestions drop-list
→ A box with the respective color and icon is created in the search field.
You can add multiple tags to the search box. Let’s look at the result pane in this case.
The result pane containsfacets,or tabs, in this case“Publications”, “Pathways”and“Diseases”, in parenthesis is the number of hits per tab:
The result pane contains alsoCards:on top are the cards of the entities being searched, followed in this case by cards of publications, pathways and diseases:
Cards are described in detail in a separate section.
For any letter you entered in the Search Box Bioseek suggests potential tag matches in a faceted drop list.
To pick up the desired tag, useUp & Down Arrowand hitENTER,or click it with the mouse. To switch between tabs in suggestions list, useCtrl + Left & Right Arrow.As we said, when atagis selecteda box with its name, icon, and color is created in the search box.
If you just hit enter after typing some text it will not be interpreted as a tag, since there might be more than one matching tag per term. You must select the tag from the drop list.
Manipulating tag priority to refine your search
When your search contains several search criteria, it is probable that you get scarce results. In this case you have the option to set different priority levels to the tags in your search:required, optionalanddisabled.This allows you to refine your search without having to delete elements of it. The system always delivers the most complete matches first. When you mark more than 3 tags as optional, one is always treated as required.
Bioseek recognisesnot only full (canonical) namesbut alsoabbreviations, old names, synonymsandaliases of any entity.
Bioseek can correct up to 2 typos per canonical name.
Each searchable entity in Bioseek is presented in a card. The card contains structured information about the entity. The information varies depending on the type of entity. For example an article card contains the title and date of publication, a list of the authors, and all entities mentioned in the article, represented as icons at the bottom of the card. These lists of related entities are made easily accessible in theInformation tabat the right side of the screen(The Right Panel),from where you can navigate further and further, exploring each group of entities to a great extent.
Here is what anArticle Cardlooks like:
The card title is the article title, followed by date of publication.
#1in the screenshot is designated the section which showsthe search criteria the article is matching;
#2is stating thenames of its authors;
#3contains icons which designate the types ofentities mentioned in this article.
All these information segments, contained in the card, are shown in detail in the Information Tab in the Right Panel, when you click the card.
Pathwaysare one of the types of entities Bioseek aggregates. The system delivers an interactive pathway image, i.e. you have the option to explore its elements further: the oneshighlighted in red are clickable.The magnifier helps you do that comfortably. You have the source link in the Information Tab, so you can navigate directly to the original source.
Using the Information Tab
The“Information”tab is the first tab in the Right Panel, followed by“Chat”, “Favorites”and“History”.
It displaysdetails about the selected entityand allows for further exploration of the entities which are linked to it, including source links such as links to NCBI, KEGG, etc.:
The related entities can begenes,diseases,articles,drugs,organisms,pathways,citations(in the case of an article), etc. For example, if you select the gene NFKB1, in the Information tab, you will get links to NCBI, a list of relatedarticles(which mention NFKB1) and a list of relatedpathways(which contain NFKB1). You can easily explore the items in these lists further, having at your disposal the same set of details for each item since each item is an object in itself, with its pertaining attributes, which are also objects with their pertaining attributes, and so on, you can drill deeper and deeper.
It is very easy to save an entity for later reference - justdrag-drop it to the “Favorites”section
All cards and tags in Bioseek are drag-droppable.You can drop an entity to the search, to the chat, to the Favorites section etc. The items in your Favorites section can be applied, by drag-drop as well, to create Visual Searches andMind Maps.You can also drag and drop items from Information, History, Favorites, and Chatto the search box.Drag-and-drop is a main operational action in Bioseek, as we aim for the easiest, most efficient proceedings.
Sorting of results
By default sorting is set tobest match to search criteriabut you can add criteria:
by date published
by number of citations, or
by number of mentioned entities:
History keeps track of yoursearchesand theitems you have viewed.Тhe special thing about the Bioseek History section is that, again,each entity in it is drag-droppable,which makes it very easy to operate with it whenever necessary - search it again, drop it to Favorites, start a Visual Search or a Mind Map (see“Drag-drop everywhere”), etc.
Advanced Search Functionality
When you perform multicomponent searches, containing 3 or more entities (genes, diseases, organisms, drugs, etc.) it is possible that you don’t find any articles, in which all three are mentioned. That is where the Heatmap comes in - itautomatically performs searchesfor articles which mentioneach possible pair of entities from your original search.The Heatmap is a table consisting of clickable boxes, in which you see the number of articles mentioning each respective pair of searched items. The darker the color of given box, the larger the number of matching articles.
When you click a box the corresponding articles are presented to you below the Heatmap and you can explore them further by clicking on the cards, as you already know.
When you select the box matching search tags A and B the rest of the search tags in your original search are automatically disabled. To use the Heatmap, you must search at least 3 entities.
Here’s a potential use case: you are searching for articles, mentioningMultiple Sclerosisand the genesHLA-DRB1andHLA-DQB1and you want to knowwhich other geneis mostly associated with these three entities. You enter these tags in the search box, you click“ANALYTICS”and, listed below,in the gene section,you see that this is the geneHLA-DQA1,which is mentioned in18 (number in parenthesis) articles together with Multiple Sclerosis and the genes HLA-DRB1 and HLA-DQB1.
To make it easier for you to quickly spot the most relevant results we implemented faceted representation of search results. We already mentioned in theDynamic Suggestionsexplanation. This grouping of results into sets is also applied in theANALYTICS,only in this case we have one more dimension -the entity additional to those in your search.It can be a gene, a disease, a drug, a process, an author, etc.
In the screenshot below we see (highlighted) that there are11 publications (number in parenthesis)which mention the disease Allergic Contact DermatitisANDthe geneFLG, 521publications which mention Allergic Contact Dermatitisandthe diseaseFacial Dermatosis, 314publications which mention Allergic Contact Dermatitisand Phenylenediamines, and so on.
BioSeek scans millions of articles and pulls out all those which mention both your initial search criteriaANDthe entities, listed in the grid.
*To update results to match newly added tags, click “REFRESH”
Alert by type of entity
You can set alert group by group as well. For example: when a new gene is introduced to thegene listwhich means, when a new article is published, that mentions a new gene along with the entities you have searched.
You want to know when thepeak of mentions of given genewas, or whothe most popular authorto write about it is, who has written on given topicmost recently,or who wasthe first to writeabout something? Bioseek can generate for you a Timeline Analysis and a Volume Analysis to visualize the number of mentions of each entity in the articles in our database, in different moments or periods of time.
The Timeline Analysisshows allpublicationswhich mention the search tags you have entered AND also mention the selected entity,in the year they were published.This GIF shows you how it works:
The Volume Analysisit is focused on thetop hits -the20 most mentioned entities,and can be retrieved year by year as well.
You can set an alert on your search to have Bioseek notify you via email about any new matching results. You can set the notification frequency to daily, weekly or monthly, which means that Bioseek will automatically re-run your query at these periods and send you emails with updated results.
You can also re-execute the search, or copy it to send the link to someone.
The Visual Search allows you to run multicomponent queries.
By drag-dropping the search boxes from the menu on the left side of the screen you can choose the types of entities you are going to search, and draw between them the connections that interest you. You have control over further specifying the entities in each position (search box) and re-execute the query.
The Mind Map is a visualization tool which helps you structure your idea. You can drag-drop any entity to it, and draw a connection you suspect exists or you search for, in order to have your idea visualized in a most clear, full and accurate way. The Mind Maps are shareable. You can set the privacy levels to each map as you wish.
The “Find links” functionality retrieves for you hidden links between the elements in your Mind Map. It is a great tool to help you perform exploratory searches. And so is theVisual Search section
Watch the full tutorial
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