Coremine Medical Help Pages

Coremine Medical gives you quick access to comprehensive information on diseases, drugs, treatments and medical biology.

When you explore concepts in Coremine Medical you access a database that is structured to relate important concepts, ranked by statistical relevance, to your topic. For example, if you type in "Alzheimer disease," in addition to retrieving documents and resources that discuss the disease, you will be able to view networks and lists that show how your query concept is related to other bio-medical concepts. This provides an overview of concepts that relate to your search as well as being an interface for navigating information on these concepts.

Other important features of Coremine Medical include the possibility to save search results and notes as well as to participate in projects on a relevant theme. By becoming a registered user of Coremine Medical you can use these tools to explore, exchange information and learn.

Table of Contents

Coremine Medical opening page

You can return to the opening view at any time by a mouse click on the Coremine Medical logo always displayed at the upper left corner of the page.

The Selection field and Categories buttons, used in selecting concepts to explore in Coremine Medical, are prominent features of the opening page and will be discussed later.

There are also several links visible on the opening page. Most of these remain constantly accessible at the top of the page throughout your navigation of the Coremine Medical interface.

The disclaimer "Coremine Medical does not provide medical advice" is included at the bottom of each page. This is to remind users that Coremine Medical is NOT intended to be a substitute for the advice of a health professional. The Terms of use link opens a page that contains the text of the full Disclaimer and other conditions relevant to the proper use of Coremine Medical.

Most of the links and buttons seen on the opening page are constant elements shown on every page within the Coremine Medical interface. A few elements, however, are found only on the opening page view.

Features seen only on opening page

When opening the web address http://www.coremine.com/medical/ the page displayed includes some text describing Coremine Medical as well as a short embedded film showing an example use of Coremine Medical.

There are also logos for various Partner and Supporter institutions that are hyperlinked to their corresponding web sites (these same links can be accessed from the Links menu described below).

This opening view is "lost" after submitting concepts to explore in Coremine Medical. You can return to the view by clicking the Coremine Medical logo in the upper left corner of any page. WARNING! this will "clear" results of the immediatly preceding exploration.

Constant elements of the interface

Links at top of page

Login

Clicking the Login text link at the top of the page opens a box requesting your Email (username) and Password. If you have not previously registered with Coremine Medical, there is a link to the Register page. If you have already registered but forgotten your password you can request a temporary new password (reset this to your own choice of password using My Page >> Profile >> Edit).

Register

The register link opens a dialog box that allows you to become a user of Coremine Medical features such as My Page and Projects. Create a nick name (to help protect your identity) and password connected to your personalized Coremine Medical pages. Registering with Coremine Medical allows you to define and create Projects, retrieve previous activity through Search History, create a list of bookmarked concepts as well as a list of concepts that trigger email alerts. There are also additional Tools for exploring and compiling a reference Library for the registered user. And participating in a Group discussion forum requires that you be a registered user.

Help

Opens these help pages.

About

Links under this menu opens to pages that describe the company and conditions for using Coremine Medical. This is a list of those links and a short description of the pages:

Feedback

Opens a page that welcomes you to submit comments and questions regarding Coremine Medical.

Links

Displays hyperlinks to web pages of selected Partners and Supporters of the Coremine Medical project.

Links to Coremine Medical function pages

Links to pages containing collections of Coremine Medical functions are visible at the upper right of any page in the interface:

Explorer

The Explorer page is the primary search and exploration page of Coremine Medical. Explorer integrates search and result viewing into one page designed to help you "build a mind map" around the concepts you seek to better understand.

Note that in addition to the Explorer concept submission field it is also possible to initiate searches in several other ways. The graphic network that appears on having submitted a query is itself an exploration tool that allows you to create new searches. Other ways to initiate a search are from Search History and other functions in My Page as well as from File upload and other functions in Tools. Each of these possibilities will be addressed in their appropriate sections.

Explorer is comprised of these primary elements:

Selection - select concepts to explore

From Selection you can begin exploring concepts in Coremine Medical. The process is like most search engines, but also includes some more nuanced features. The simplest example is to select one concept to explore. But you can also select several concepts to explore simultaneously. Another nuance is the ability to limit the selection of concepts to specific categories. In addition, there is the possibility that the concept you wish to explore is missing from Coremine Medical dictionaries, in which case you will be prompted to report the concept to Coremine Medical experts to be considered for possible inclusion in future dictionaries.

Finally, there is an option to select among the names of experts. To illustrate this idea, notice that an example concept, "Influenza," and an example expert "Edwards, RG" are shown in connection with Selection. Concepts and Experts are two fundamentally different approaches offered by Coremine Medical: you can either select concepts from biomedical dictionaries or authors of scientific papers (Biomedical experts).

Select one concept to explore

Note that suggested concepts appear in a list below as you type. These concepts are drawn from the dictionaries used by Coremine Medical. Each suggested concept belongs to a category relevant to health and medicine (choosing concept categories will be discussed later).

Continue typing characters while inspecting the list to find the concept you wish to explore. The suggestions may also include names of biomedical experts recognized as authors of scientific articles.

Also, Coremine Medical dictionaries include synonym matching. Sometimes a commonly used concept differs from a more correct concept. For example, typing "cancer" will show "Neoplasms (alias Cancer)."

Once you have identified the concept that you wish to explore, use a mouse click or the enter key to include it to the selection box. Additional information shown with the selected concept is the category - that is, whether the selected concept represents a disease, drug, etc. - and the number of connections made by the concept. The "connections" number indicates how many other unique concepts co-occur with the selected concept. More about how Coremine Medical assigns and ranks connections between concepts will be discussed under the Extracted knowledge section.

When you click the Explore button, Coremine Medical will display a Network ("Concept Map") around the submitted concept as well as text and links relevant to that concept.

Select several concepts

Coremine Medical is designed to allow you to readily expand your search to include several concepts and explore the intersection of concepts.

If you already have the results of a search visible the Explorer window, you can bring the selection panel back into view using the "Click here to modify your search" tab near the top of the screen. The similar tab "Click here to cancel" will return you to search results will return the results view without initiating further action.

If the Selection input fields is visible, simply repeat the process just described to add more concepts to be explored together (type text into the input field and choose from among suggested concepts). concepts added will appear in the selected concepts box.

Notice that selected concepts include check-boxes that allow them to be deactivated or reactivated as part of the focus of an exploration. Also, there are controls "All|None|Delete select" at the bottom of the box that initiate the indicated action on the check-boxes and selections.

Select concepts from specific concept categories

As suggestions are shown while typing in the Selection input field, a text link ("Filter...") appears below the concept entry field (to the right of the text Choose one of the concepts to explore:). If you choose to open the filter you will see a list of concept categories. By default, concepts in all categories are used to provide a match to the text you type. If you wish to limit concepts to a specific set of categories you can do so by using the associated check boxes. concept suggestion categories include:

Each category is a list of biomedically relevant concepts and associated synonyms. The source of each concept type is described below under the heading Categories.

Once having changed settings, click the "Update suggestions" link to apply the filter to the suggestions that appear in the concept entry field. The filter will remain in effect throughout your explorations session unless you choose to change it.

Report a missing concept

There are times when a legitimate and useful concept does not appear among the suggestions offered while typing a concept into the input field. A dialog box will appear whenever Coremine Medical is unable to suggest a concept in response to the text you have typed. In this dialog are suggestions for how a match might be achieved, but also a text-link stating "please report the missing medical concept or biomedical expert to us here!"

The link will open a new dialog box that allows you to submit the suggested concept to Coremine Medical experts for review and possible inclusion in and updated dictionary. The dialog box includes fields that allow you to write the missing search phrase and a comment. There is also a menu that can be used to select a concept category that you believe is appropriate for the concept. In addition, you can enter an email address if you would like to be contacted regarding the review status of the concept you submitted.

Although Coremine Medical dictionaries are drawn from sources like the Medical Subject Headings (MeSH) thesaurus of concepts and other large dictionaries addressing biomedical concepts, some important concepts may not be included in these source materials. Sometimes even fairly common concepts are missing because these may differ from a stricter use applied by experts. Other times there are acronyms or other variants used by one group of specialists that are unknown to another group. We appreciate the input of our users any time a missing concept is brought to our attention.

Select an expert

If you know the name of a Biomedical expert, you can use Coremine Medical to search for that expert and colleagues.

Alternatively, if you wish to find an expert in a given field, use keywords to search within the field and then view the Biomedical experts list to be discussed in the section on the Focus panel under Extracted Knowledge.

To search for an expert from the selection menu, begin by typing the last name of the expert. A list of suggestions will appear. Add first name initials if you need to refine the search to fewer suggestions.

If the expert name does not appear you may choose to report the missing name to our experts for evaluation, as described above regarding missing concepts for concepts.

Categories - choose concept categories

The icons under the text "Categories (click to disable)" are "switches" that allow you to limit the scope of your search results to concepts within various concept categories.

To illustrate the function of these category filters, consider the question "how is breast cancer treated?" To explore possible answers to this question, and to avoid suggestions outside of its scope, you can choose to leave only the Drug and Procedure categories active (click all other categories to "gray out" their icons). Now you can type "breast cancer" in the Selection field and you will see the concept "Breast carcinoma" suggested as a match.

The concept map generated by this process would show one Disease concept (Breast Carcinoma) and five concepts each from Drugs and Procedure categories. The search concept will always be included, even if its category is "deselected" (in the case of this example, Breast Carcinoma, by virtue of it being the search concept, is included even though Disease category concepts are excluded from search results).

Note that these buttons affect the types of concepts that will be retrieved once you have clicked the Explore button and launched a search. The Categories buttons do NOT change the concept suggestions seen during concept selection (see Select concepts from specific concept categories for a description of that process).

The concepts used by Coremine Medical to identify concepts and other entities in scientific and popular literature make up dictionaries of recognized concepts compiled from trusted sources. Concepts can be assigned to higher-order groupings and Coremine Medical operates with twelve such categories that can be used to define your search.

Below is a list of the biomedical concept categories used by Coremine Medical and an indication of the sources used:

DO: Disease Ontology
Drug Bank: Drug Bank
EG: Entrez Gene
GO: Gene Ontology
GP: GoldenPath
HG: HomoloGene
iP: iProclass
MeSH: Medical Subject Headings
RS: RefSeq (*.protein.faa.gz files)
UG: UniGene
UMLS: Unified Medical Language System (an aggregator of primary sources including MeSH and DO)
UP: UniProt
USDA: United States Department of Agriculture
ZM: ENZYME

Network

A Coremine Medical network images is composed of concepts related to your search. The image is both a "concept map" of connected concepts and a tool for navigating the concept space implied by your search concepts.

The network image will appear after making a selection and clicking the Explore button. If your browser does not present a network image, please check that you have installed a Flash Player plug-in (visit http://get.adobe.com/flashplayer/ to download free of charge).

The initial network image shows concepts clustered by concept type. A mouse click on a cluster will expand these to show individual concepts.

Mouse actions allow other interactions; the network is interactive in several respects. First of all, mouse functions allow you to explore and dig into information represented by the individual elements of the network. Mouse over a network node (a "bubble" containing a concept) to see associated information (like the number of connections associated with the concept and the concept type category to which it belongs). Similarly mouse over on an edge (line connecting nodes) to show how many articles are shared by the connected concepts. Clicking on an edge or node allows you to re-focus to that particular element (how this affects the Focus panel content such as the Extracted knowledge, Related articles and User updated content will be described later). Mouse over on a node shows a "down arrow" triangle that can be clicked to suggest a set of actions, such as setting a Bookmark for a concept or launching a new search with that concept.

These are the primary elements of the Network panel:

Add a concept to the Network - insert another concept

At the upper-left of the Network panel is an input-field that allows you to add concepts to the network image. Concepts submitted through this field will be incorporated into the existing network (in contrast to those submitted from the Selection input field which results in launching a new search with selected concepts).

Category filter - remove categories of concepts

Clicking the buttons under this menu causes concept types to be removed according to category. Clicking the same buttons a second time restores those concept types. (Note that concepts used in the query are not removed regardless of the concept type category to which they belong).

Network Tools - set viewing and other options

Choices under this menu allow you to modify views of the network.

Grid view - change network to table

This changes the presentation of the information in the network to table form. Note that you can also find an exhaustive tabular presentation of concepts under the Extracted Knowledge headings.

Network view - change table to network

When the image is in Grid view, clicking the Network view button under the Network tools menu returns the presentation to network form.

Fullscreen - causes image to occupy entire screen area

Save - stores information in My Page Bookmarks

Registered users can use this function to store results of the network when logged in. If not logged in, clicking Save will open a login window with the option to register as a Coremine Medical user.

Find in network - text search in network

Allows search for a concept within the network based on the spelling of that concept.

Filter by connection relevance - limit items displayed by statistical significance

The slider bar adjusts which connected concepts are visible in the network based on the statistical significance of their connection.

Mouse mode - choose between move and select modes

Move and Select options allow different mouse actions on the network image. The differences in action are seen when the mouse-pointer is placed on the network image panel on the gray, background area (any part of the panel not occupied by a network node or edge).

In Move mode (the default mode), click and hold allows you to drag the entire network image from place to place.

When Select mode is chosen, click, hold and drag causes the mouse pointer to select network nodes within the rectangle described by the drag motion.

In both move and select modes, when a mouse-click is initiated on a node or edge in a network, the focus concepts change. In the case of an individual concept, the node clicked will become slightly larger and will gain a yellow border. For an edge, the click will cause the edge color to darken and a triangle "down-arrow" will appear at its midpoint (more about the down-arrow in the section Action menu on Edge).

Also in either mode, when the mouse pointer is placed on a network node and the mouse button depressed and held the node can be repositioned within the graphic.

Annotate Network - add concepts to each node in network

The Annotate function connects more concepts to each concept node in the network (in as much as such connected concepts are found). Clicking Annotate network opens a menu that allows you to choose a concept type category. After selecting a category click the Annotate button at the bottom right of the menu and the network will be modified to include new nodes from the category.

Best Fit - automatically rearrange network elements

Clicking the Best fit button moves network nodes to evenly spaced positions around. WARNING! Best fit will remove manual rearrangements made to nodes. If you have moved nodes around and you wish to keep them in their moved positions do NOT click best fit. Best fit is also invoked every time a concepts clustered under their concept category are opened.

Highlight - cause mouse-over action to highlight connected nodes

The Highlight option is most useful for complex network created when several concepts are submitted simultaneously. The purpose in a complex search is often to find which concepts intersect. Choosing Highlight causes mouse-over of a network element to visually emphasize the nodes and edges that are directly connected. This can be an aid in finding which nodes connect to several concepts and identify such intersections.

Choose the Highlight option and move the mouse-pointer onto a network node. Notice that all elements in the network except those directly connected to this node will dim but connected nodes and edges remain in strong color.

Actions on Network or Grid - mouse-pointer initiated actions

Elements of the Network and Grid allow you to initiate actions with a mouse.

In the Network image, clicking a node or edge changes the focus to the selected concept space. Each node also has a "down arrow" triangle that becomes visible on the upper right side of the node when under the mouse-pointer. A similar arrow appears at the mid-point of an edge. Clicking this triangle opens a menu of possible actions that can be initiated.

NOTE! In the initial presentation of the network, your search concept appears surrounded by clusters of concepts under their category names. In each category are the top concepts (as judged by Coremine Medical algorithms) connected to your search concept. A mouse-click on any cluster will "unstack" the nodes representing each concept in the category.

These are the actions that can be initiated with the mouse pointer in Network and Grid view:

Change Focus Concept - select concepts or connections to redirect information displayed in focus panel

Mouse-click on a network node or edge to redirect focus. That is, in the panel to the right of the network image under the heading "Based on your focus" is information pertaining to the focus concept. Clicking on a network node or edge causes the panel to be populated with information pertaining to that node or edge.

Notice also that by clicking a network node that it acquires a yellow border to indicate that it has been selected as the focus. Node borders may also be red, indicating that they represent the concepts submitted in the search. Nodes with a white border are those that were not among the submitted concepts. Clicking nodes with either white or red borders causes the concept to become the focus.

When an edge between two nodes is the focus concept it will appear as a red and black dashed line. Notice that both concepts will appear in the Focus panel. In a similar way to the border colors used on nodes, edges connecting concepts that were included in the search submission appear in red, while all other edges appear in a gray tone.

Action menu on Node - activate options pertaining to concept shown in network

The "down-arrow" triangle is seen at the upper right of a node when activated by the mouse-pointer. That is, mouse-over of a node causes the node to expand and the triangle to become visible. Clicking this triangle causes a menu to open with the following action possibilities: Select; Expand; Remove; Open in new search; Add bookmark; Set alert.

The actions Remove, Open in new search, Add bookmark and Set alert can each be applied to an individual node (this concept) or all selected nodes (the selected concepts). Nodes can be marked for as selected using Select action in the menu. Nodes can also be marked as selected using the Network tools Mouse mode Select option discussed earlier.

Select node - labels node for future action

By clicking Select the concept represented in the node is selected for future action. Note that a yellow border appears on the node when selected. Yellow borders also appear when a node represents a focus concept. However, the Select action does not cause the content presented in the focus panel to be redirected to the concept in the selected node.

Expand - find more connections to concept

Expand appends additional concepts to a concept node. Click Expand to open a menu box. The menu lists concept types, each with a slider bar for selecting the number of concepts you would like to add. Adjust slider bars as appropriate and click the Expand button at the lower right of the menu.

Remove (this concept/selected concepts) - removes concepts from network

Removes the node (or all selected nodes).

Open in new search (this concept/selected concepts)- creates new network around concepts

Opens a new search with the selected concepts, replacing the current network with the results of the new search.

Add bookmark (this concept/selected concepts) - adds concepts to Bookmarks in My Page

Bookmarking a concept helps you find this concept again in the future. Bookmarks are stored in a table under My Page, Bookmarks.

Set alert or Modify alert - add or modify alert status for concept

With Set alert you can choose to receive email alerts on new information pertaining to the concept. If alerts are already activated the menu will show the Modify alert option, allowing you to change the alert type or to remove the concept from list of alerts.

Action menu on Edge - activate options pertaining to concept shown in network

Focus - change focus to intersection of concepts

This action changes the information presented in the Focus panel to include the connected concepts (it has the same effect as clicking the edge anywhere outside of the down-arrow). At the top of the panel you will see the names of both concepts. In the Common extracted knowledge section are concepts that are associated with both concepts. Similarly, under Common related articles and hits are articles, websites, etc. that discuss the connected concepts. Common user updated content shows context notes submitted by user on the intersection of the connected concepts.

Open in new search - launch search based on the two connected concepts

Here a new search will be launched and a network created that includes concepts associated with either of the connected concepts.

Set alert Modify alert - add or modify alert status for intersection of concepts

Clicking Set alert will initiate email messaging when new information becomes available on the connection of the concepts. Once an alert is set on the connection, the option shown will be Modify alert, in which case you can decide to change alert status or remove the alert entirely.

Search history links - retrace recent search results

Directly below the network image is a short list of recent search items. You can click on any of these to return to results obtained earlier searches.

A more complete history of searches can be found under My Page Search History.

Focus panel

The panel to the right of the Network contains text, links and, in some cases, images relevant to your focus item. At the top of the panel you see "Based on your focus" (your concept or expert) "...we found the following information" indicating the content of the panel. Information presented in the focus panel includes a summary Facts, Extracted knowledge, Recent articles and hits as well as User updated content. There is a also a SHARE button at the top left of the panel that provides links to email and social media options for sharing search results from Coremine Medical.

SHARE

You may want to send Coremine Medical result content through an email or post it to Facebook or other social media. Clicking the SHARE button opens a list of links that enable these sharing options. Choose an option and follow instructions as they appear to share content in this way.

Bookmark/Alert

Bookmark and Alert functions allow you to save concepts in a list as well as to receive email notices when new information on the concept or connection becomes available.

Clicking the star-shaped icon adds the focus concept Bookmarks list in My Page. Once a concept is bookmarked, the star icon will be colored yellow in the Focus panel.

Clicking red text Set alert! opens a dialog allowing you to choose alert options. Concepts and connections you have chosen are listed in a table under My Page Alerts. You can modify alert status from this table or from modify alert (blue text) which appears next to the star icon when the focus term has been selected for alerts.

Synonyms

There are often alternate names, i.e. synonyms, for scientific concepts. In the Focus panel below the primary name for the concept is the Synonyms blue text-link. Next to the link is a number in parenthesis. This number indicates how many synonyms Coremine Medical recognizes for the concept. Clicking the link opens a list of these synonyms.

Facts

Text and links at the top of the Focus panel show summary facts on the focus item.

The type and amount of information presented depends on the nature of the focus item - whether it is a concept (i.e. a biomedical term) a biomedical expert or the information that is common to concepts or experts. The focus item is indicated as a "bubble" (or two "bubbles") just below the text "Based on your focus" near the very top of the pane. If you are exploring concepts you will see the corresponding biomedical term in the bubble image colored according to its concept category. Biomedical expert bubbles have a charcoal-black background and show the last name of the expert followed by his first initials. Two bubbles are shown in this space when the focus item is an "edge" between connected concepts or biomedical experts.

Just below is the text "...we found the following information" and a dividing line. Below the dividing line is the summary information on the focus item.

Facts content according to focus item types are as follows:

Disease Facts - Facts presented when Focus item is a Disease Concept

Disease facts are extracted from information compiled under the Unified Medical Language System (UMLS) that draws form other sources including the Medical Subject Headings dictionary (MeSH), the National Cancer Institute (NCI), the National Library of Medicine Medline Plus, the Diagnostic Statistical Manual of Mental Disorders (DSM-IV) published by the American Psychiatric Association and others. UMLS is part of the National Library of Medicine (NLM) at the US National Institute of Health (NIH). In some cases information is also gathered from sources outside the NIH, such as the

Clicking the link More facts opens links to information under these group headings:

Drug Facts

Most of the information in the Facts panel for a drug is extracted from Drug Bank and include the following at the top of the panel:

Primary name of the drug - Normally, this is the "generic" name assigned as an International Nonproprietary Name (INN) by the World Health Organization intended to unambiguously identify the active ingredient.

Synonyms - Other names for the drug, including brand names and in some cases names used during drug development.

Description - A short description of the drug.

Clicking the link to More facts below the description opens these headings:

Drug Properties

Includes Chemical formula, Category, Type, ATC code, and a list of Brand names.

Indications

Describes pathologies that the drug has been approved to treat - that is, the diseases that are normally treated with the drug.

Mechanisms of action

A description of how the drug affects molecules in the body (if this is known). In most cases, drugs interact with cellular proteins and block their activity in some way. Drugs may also interact with DNA or RNA or other molecules.

Metabolizing Enzyme

The enzyme or enzymes that degrade the drug molecule (if known). In some cases, drugs are not metabolized but leave the body through urine.

Targets

The biological molecules that are influenced by, and give rise to, the pharmacological effect of the drug (when known). The primary target of the drug is usually mentioned in brief under the heading Mechanisms of action. Targets listed might also include other molecules that are known to "bind" the drug, whether or not the pharmacological effect of the interaction is not known or intended.

Drug targets are normally listed by their corresponding human gene name. When the drug is an antibiotic the target will be a molecule associated with the pathogen and named by its corresponding gene. In some cases (such as for many anticancer agents) drugs interact with DNA (hindering cell replication) in which case the target will be listed simply as DNA.

References

Coremine Medical incorporates some of the links to external references extracted from Drug Bank.

Symptom Facts

Symptom Facts are from the Unified Medical Language System (UMLS), at the US National Institute of Health (NIH).

Clicking the link More facts opens links to information under these group headings:

Procedure Facts

Procedure Facts are from the Unified Medical Language System (UMLS), at the US National Institute of Health (NIH).

Clicking the link More facts opens links to information under these group headings:

Anatomy Facts

Anatomy fact sources include the Unified Medical Language System (UMLS) and the Medical Subject Headings (MeSH), at the US National Institute of Health (NIH).

Clicking the link More facts opens links to information under these group headings:

Food Facts

Information shown for Food focus items is that name of the food and synonyms of that name.

MeSH Facts

MeSH facts are drawn from definitions at the Medical Subject Headings structured dictionary and its (MeSH) at the US National Institute of Health (NIH).

Clicking the link More facts opens links to information under these group headings:

Chemical Facts

Information shown when a concept from the Chemical category is the Focus item is the name of the chemical and synonyms of that name.

Cellular component Facts

Information presented when a Cellular component is the focus is sourced to the definitions within the structured database at The Gene Ontology GO. This can include a definition of the concept, synonyms and its place within the GO hierarchy (click the link More facts to open information under the hierarchy heading).

Biological process Facts

Information presented when a Biological process is the focus is sourced to the definitions within the structured database at The Gene Ontology GO. This can include a definition of the concept, synonyms and its place within the GO hierarchy (click the link More facts to open information under the hierarchy heading).

Molecular function Facts

Information presented when a Molecular function is the focus is sourced to the definitions within the structured database at The Gene Ontology GO. This can include a definition of the concept, synonyms and its place within the GO hierarchy (click the link More facts to open information under the hierarchy heading).

Gene/Protein Facts

The information shown in Facts for a Gene/Protein focus item includes the primary symbol for the gene, the name of the protein for which it codes (normally), a list of synonyms and a description of the function of the protein. The main source of this information is the Gene database at the National Center for Biotechnology Information (NCBI) under the National Library of Medicine (NLM) at the US National Institute of Health (NIH).

Clicking More facts opens more information on the Gene/protein in focus under these headings:

Homology - similar protein sequence

Shows a list homologous Gene/proteins identified in other organisms (includes Gene/proteins found in organisms addressed by Coremine Medical).

Pathways - metabolic or other pathway role

The molecular-biological role of the protein as assigned by the Kyoto Encyclopedia of Genes and Genomes (KEGG). Under the Pathway heading are web addresses named in relation to the various metabolic, signaling or control functions associated with the Gene/protein in focus.

References - Sequence records

Under this heading are links to Protein (amino acid) and DNA or RNA (nucleotide) sequences at (NCBI) including UniGene as well as the UniProtKB, a protein database under a consortium comprised of the European Bioinformatics Institute (EMBL-EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource(PIR) associated with Georgetown University Medical Center.

Biomedical expert Facts - information pertaining to an expert

When a Biomedical expert is in Focus, facts shown include the family name and initials of the expert as well as the number of articles that include the expert's name among the author list. In addition to these basic facts is information grouped under the following headings:

Keyword profile - concept keywords extracted from publication list of the expert

Keywords (Biomedical concepts) found in the publication list of the expert. These appear in a table and are ranked according to statistical significance. The table includes keywords at the left and a graphic representing statistical significance to the right in each row. The graphic is made up of 10 rounded rectangles. Blue filled (versus gray) indicate "strength" in the association between the expert and the keyword in the corresponding row. That is, if the expert appears as an author on a lot of papers that include the keyword there is a strong association.

Placing the computer-mouse cursor on the row of rounded rectangles (the graphic) will cause a mouse-over display to appear. The display shows the numerical significance of the association between the expert and the concept. The lower the number, the greater the significance (the number can be thought of as a p value). The values of greatest significance are often rounded to zero and rank at the top of the table.

The significance values used to rank keywords (Biomedical concepts) in the table are calculated using a function based on the frequency with which the keywords appear within the experts body of publications versus that of other authors.

Recent research articles (PubMed) - list of articles by the expert

Articles that include the name of the expert in the list of authors found in MEDLINE (PubMed) listed in a table with most recent articles at the top.

Publishing timeline - when articles by the expert were published

Under this heading is a bar graph showing the number of publications attributed to the expert on any a given year. The graph includes scroll arrows to the right and left.

Biomedical experts working with similar subjects - list of authors with similar keyword profiles

This shows a table with author names juxtaposed to a significance score graphic (rounded rectangles) to the right in each row. Significance in this case is related to the common keywords in each expert's publication list. Blue (versus gray) rectangles indicate statistical "strength" and mouse over of the graphic shows a numerical significance value. Values close to zero indicate greatest significance and ranking toward the top of the list.

Concept intersection Facts

When an edge between two Biomedical concepts is selected as the focus item the facts panel is populated simply by the names of these items and their concept categories.

Biomedical expert intersection Facts

When an edge between two Biomedical experts is selected as the focus item the facts panel is populated by the family names and initials of each expert as well as the number of MEDLINE (PubMed)articles that include the expert among the author list.

Below the author names is information under these two headings:

Common Concepts

A list of Biomedical concepts (Keywords) associated with the authors and ranked using an algorithm that takes the body of work from each expert into account.

Common PubMed Articles

Lists all MEDLINE (PubMed)articles that include both of the experts among the author list.

Extracted Knowledge - by way of mining scientific literature

The extracted knowledge panel lists concepts (either Biomedical Experts or Keywords) that are related to the focus concept. These are essentially tabular versions of the information presented in the Network, except the tables usually contain many more concepts than would be practical to represent in graphic form (note that the concepts appearing at the top of the table are the same as those seen in the network). Concepts are judged to be related based on the knowledge extracted through text mining of scientific literature.

Biomedical experts - authors of articles

Here a list of biomedical experts is suggested for the biomedical keyword in focus. Biomedical experts are suggested based on their keyword profiles.

To understand how this works, consider that keyword profiles are lists of biomedical concepts identified from the publications of each expert (that is, the text made available in MEDLINE for each expert). Each keyword in an expert profile is given a p-value reflecting its significance to the expert (a function that considers uses by the expert versus independent use of the keyword is used to calculate the p-value). Experts are ranked in the list based on their p-value associated with the focus keyword. When more than one keyword is in focus, an averaging function is used to calculate a ranking for each expert.

Related concepts - found together in articles

Here, information related to the focus item is arranged by category, where entities in each category appear in a ranked table. The information presented in the tables has been extracted from MEDLINE records obtained from National Library of Medicine (NLM) using the algorithms developed for Coremine Medical by its creators. In brief, the algorithms index Biomedical concepts (i.e. Keywords) and author names to individual MEDLINE records. This information is used to cross-reference the entities to one another. Furthermore, "counts" of entities in relation to one another and their associated records are used to calculate a statistical score for the association between the two entities using a function that considers the frequency with which the entities co-occur versus their independent occurrence in the corpus as a whole.

The tables are structured in the same way for each concept (category. At the right side of each row is the name of extracted entity (either a Biomedical expert name or a Biomedical concept). To the left in each row is a graphic indicating the statistical significance of the association between the focus item and the extracted entity. The graphic is composed of ten rounded rectangles where blue fill (as opposed to gray fill) indicate the level of significance.

Mouse-over action on the significance graphic (the rounded rectangles at the right side of each row) causes a box to appear showing the significance score calculated between the focus item and the extracted entity.

Low scores indicate high significance. That is, the significance score is a measure of the frequency with which the number of actually observed co-occurrences between the focus item and the extracted entity might be observed if each was randomly assigned to any record in the MEDLINE corpus. In other words, the significance values is a probability that the observed level of association between the focus and extracted entity is a result of chance.

Extracted entities with very low scores (lowest probability that they are chance occurrences) are therefore ranked toward the top of the table as being most probably truly related. In some cases, significance scores shown may be so low as to have been rounded to zero.

Related articles and hits - lists and links to scientific articles and other sources on the web

Under Related articles and hits are lists of resources that Coremine Medical has used to find documents relevant to the concept in focus. These include the National Library of Medicine MEDLINE records found at PubMed as well as several other sources of information available through the internet.

The full list of resources can be seen by clicking the link Show more web sources seen under the top headings. Under each heading is a list of documents and a hyperlink to the document (e.g. click the Recent research articles heading to open the list and then click an entry to open the PubMed page that contains the abstract for that article).

These are the various web resources that Coremine Medical examines to find Related articles and hits relevant to a focus concept:

User updated content - user comments

As the title implies, the entries under this heading are those added by users like yourself. As is the case for all items shown in the Focus panel, the content shown is that which has been connected to the Focus concept. But here the connection to the Focus concept has been made explicitly by a user rather than having been discovered through Coremine Medical algorithms as would be the case for the connections shown under Extracted knowledge and Related articles and hits.

Information shown under User updated content is user comments. Opening the Comments section shows notes added by other users and also provides a form for adding your own comment.

You can add content here only if you are logged in as a registered user of Coremine Medical (see Login for help on creating an account and logging in as a user).

Viewing and adding comments to your focus concept

Clicking this section shows comments added by users and also shows the dialog Add new comment on... with fields for submitting a new comment. Notice that you can either leave notes open to anyone or limit their visibility if you wish: Visible for -

If you leave the radio button selection for Everbody, the comment you add will be visible to any user. The Only you option will hide the comment from all viewers except you when logged in under the same user profile (that is, using the user name and password that was active when you added the comment).

Notice that comments added by the user appear in the context of the focused element in the network. That is, a comment is shown only when its associated node or edge is selected in the concept-map, regardless of the visibility level selected.

You can contribute with comments in two ways; either by adding a new comment or commenting on an existing.

If you wish to reply to an existing comment, click the comment name and further the appearing Reply button. The visibility of your reply follows that of the original comment.

My Page

My Page is a "personal workspace" that can be used to store information gathered while exploring and build your understanding.

Most of the features under My Page become active only after you login as a registered user. Once logged in you will see the following tabs in the My Page pane:

Search History - review searches

Search History opens a list of recent Searches presented in a table. The content of the table is presented in chronological order (most recent Searches at the top). The table has three columns: Date, Origin and Your search. Entries in the Origin column show the general class of search (whether it was launched using a concept or Expert, for example). The entries in the Your search column list the search words used.

At the bottom left corner under the table is a statement of the number of searches recorded in your history. If you are not logged in as a registered user, Search History will only list searches from the immediate session. User login brings up all previous searches made under your registered name.

At the center just under the table is a page browsing gadget, and to the right of that a Go To Page submission field allowing you to type in a desired page number.

To re-run a search, use the mouse-pointer to click the desired row in the Search History table. Note that the row is highlighted after clicking. Once highlighted, click the Re-run selected button (green) at the bottom right of the panel.

Bookmarks - view and manage saved concept-maps,concepts, expert names and documents

Bookmarking items of interest while exploring helps you to remember concepts and to find these later when you return to Coremine Medical.

From the Bookmarks pane you take several actions: View bookmarked items; Activate email alerts; Share item; Comment on bookmarked item; Delete Bookmark; Launch search in Explorer with bookmarked item.

View bookmarked items
Bookmarked items are listed in a table. That is, concepts, Biomedical expert names and Documents saved from Explorer Actions menus or the Focus panel Bookmark (star shaped button) will appear in the table.

Above the table is a search field as well as filter options. The search field can be used to search for a bookmarked item within the table. Filter check boxes can be used to limit which types of bookmarked items are displayed in the table: Concepts (i.e. biomedical terms); Biomedical experts; Documents (MEDLINE records).

The Bookmarks table has six columns with these headings:

Clicking any row to select and opens details of the item in the space below the below the table. If the item in the table row is a Concept, the details shown will include the concept name, category, synonyms etc. much as in the Focus panel from Explorer. In the case of a Biomedical expert you will see the name of the expert and number of articles in PubMed. For a Document the information will include the title, source and abstract of the article.

In each case, the comment field will be visible and show previous comments you have entered.

In the case of Concepts and Documents there is the option to set alert triggers such that email is sent to you when new publications become available.

Activate email alerts You can activate email alerts on an item previously bookmarked. (Note that you can also activate email alerts from Explorer Actions menus or the Focus panel Alert.)

Click anywhere on the row of the item that you wish to target for alerts. Scroll down to see the details on that item below the table. Note the red text Set alert! Clicking this text opens a dialog box that offers alert options. Save these options to begin receiving email alerts on this item. Note that the red text has been replaced by the blue Modify alert. Modify alert allows you to change alert status. Notice also that the table will now show the green text Yes in the Has alert column of the selected item.

Share item Clicking this text in the table will open a dialog box that allows you to share the selected item with a Group discussion (see Bookmarks in Group).

Comment on bookmarked item
Below the table is a field that accepts comments to be added to the selected concept.

Delete bookmark
The Delete bookmark button is found at the lower right corner of the Bookmarks page. Clicking this button deletes the selected item from the list of your bookmarks.

Launch search in Explorer with Bookmarked item
The Show network button is found at the lower right corner of the Bookmark page. Clicking this button launches a search with the selected item in your bookmarks table. If a Document was selected from the bookmarked items the button will instead appear labeled as View article with the corresponding action.

Alerts

This tab shows items from your Bookmarks associated with e-mail alerts. Use the "Edit" button to change the parameters and status of alerts.

Notifications

Here you can view activity on Alert items. There are two tables shown.

In the top table is a list of the items that have triggered an alert in the last round of data update to Coremine Medical. In this table you will see the date that the alert was triggered, the subject (alert item) and the type of notification (that the notification regards an alert item).

In the lower table you will see a list of articles where each row contains the PubMed Identification Number (PMID) and the title of the article. The PMID forms a hyperlink that will open the article abstract in Tools>Library>View Document.

Profile

Under My Profile you see a box describing information about your Coremine Medical account. Click the "Edit" button at the bottom of the field if you wish to make changes to this information. In edit mode you will see three editable fields in the Personal information box:

Your "Nick" (nickname) is the name that appears on comments and project member lists. The Name field is the name you chose for yourself that is only shown to you and in projects you are a member of. The Email field is the Email you chose when you registered with Coremine Medical (editing this will change your login username as well since these are identical).

The text link below these fields allows you to Change password.

The "Occupation" field contains a list of possible occupations as well as the option to enter "Other".

Projects

Here you can create projects or view the latest activity in your existing projects.

It is easy to both save, share and comment content you find in Coremine Medical using the project module.

Tools

The Tools page is comprised of the following elements:

Library

The Library tool helps you search PubMed, create a list of articles and export your list to a file to be stored on your computer hard-drive. You can also import a file from your hard drive and display it in a table. In addition, lists of articles can be used to form a Concept map and Focus in the Explorer window.

When you click the Library link on the Navigation bar in Tools a panel will open with four options:

Document Search - Search with a Concept or Expert name to generate a list of articles

In Document Search you can launch a query with one or several Concepts (much as in Explorer Selection). Similarly, you can search with one or several Biomedical expert names. To add Concepts or Biomedical experts to your search, use the submission fields in the box with the heading Add search concept.

The Concept or Biomedical expert list you create will appear in the box headed Your search. Note check boxes allow you to select or deselect concepts and that you can manage the concept list with the All None and Delete selected action links at the bottom of the box. The items in your search can be combined using the boolean operators 'AND' and 'OR' below the search box.

Once you have chosen your desired query concepts, you can launch the search by clicking the Submit button. The result table holding the PubMed articles will appear below the Submit button. The table holds a maximum of fifteen articles per page. Page navigation is found at the bottom of the table.

The result table is comprised of nine columns:

View Document - View a document

The abstract for an article appears in the View Document pane after having clicked its PMID in the result list table.

In addition to the abstract text, View Document shows the article PMID, its Title, its Biomedical expert (first author), the Publication (with volume, issue, etc.) and the Year that it was published.

Other attributes of View Document are

The Concepts table is comprised of two columns: Name and Category. The Name column shows the concept and Category lists the concept type.

Library basket - Import or Export a list of articles or generate Explorer search with concepts found in article list

Functions for importing and exporting lists of articles are found under this Library tool (uploading concepts files is another function discussed in File upload). There are four buttons in the Library actions group at the upper right of the Library pane: Empty; Import; Export; Network; Cluster.

Empty: Clicking this button simply removes all content from the Library basket. WARNING! There is no undo button for this action. The Library basket may contain hand-picked articles selected from the List of articles pane. In this case you would have to repeat this process to reconstruct the list.

Import: Three file types can be imported to the Library basket:

EndNote files are those compatible with the reference management software package of that name (see http://www.endnote.com/).

You can create comma separated PMID files in a number of ways. These should contain PubMed Identification numbers separated by commas only. When these files are viewed in a text editor they should appear as a column with each row containing only the PMID and a comma, or as a string of PMIDs separated by commas or white spaces, e.g.;

21596533,
21559387,
8725745,

or

21596533,21559387,8725745,

Files should end in .txt or .csv extensions. These can be generated in a number of ways, perhaps most commonly using Microsoft Excel through Save As>Other formats>Save As Type>CSV (Comma delimited)(*.csv).

Export: Library tools can also be used to create lists of articles for export. You can create a list by choosing specific articles from a PubMed search. Do this using Add to basket from the List of articles pane. On opening the Library basket pane you will see the selected articles in a table. Click the Export button to generate a file from the articles selected to the basket. Two types of files can be created in this way: These file types are compatible with versions of the EndNote reference management software package (see http://www.endnote.com/).

Files exported as Endnote XML can be re-imported into Library basket, using either the EndNote X1-3 XML or the 8-X setting. XML files are also readable by a number of other software products.

Files exported as Endnote ENW cannot be retrieved to the Library basket.

Network: This function identifies all biomedical concepts found in your collection of articles and uses these to create a new search and concept map in Coremine Medical Explorer. In other words, Coremine Medical searches for recognized concepts within the body of text that you have gathered into the Library basket. It can then launch a new search using the found concepts.

On clicking the Network button you will be able to choose among the following options for network creation: That is, you can choose to launch a search directed only at the articles selected in your list, or send the search to the complete set of PubMed (MEDLINE) articles. Also, you can choose which concept categories (Disease, Drug, etc.) that should be used in the search (as in the Selection feature in Coremine Medical Explorer).

Click the Create button at the bottom of the dialog box once having selected the options you wish to apply to the search. The Explorer pane will open showing a concept map of the concepts extracted from the articles in your Library basket. Clicking on any concept in the network will direct the information in the Focus panel to that concept.

Cluster: This feature will help categorize and group the articles in the Library basket.

Clustering Results - Holds the results of article clustering, where sets of up to 1000 articles are grouped into clusters based on similar text content

Each clustering result created from the Library basket pane will be stored in a table here as long as you are logged in. Clicking a clustering row will make the details of the various clusters appear below the table. You will find the five key words best describing each cluster, all article titles are shown and the ten best descriptive cluster sentences are displayed. Each clustering row has an 'Explorer' link in the right-most column. Clicking this link will display the clusters as nodes in the Explorer pane. By navigating the network, you can also get to each cluster's Concepts, from where you can choose to explore concept networks.

Sequence Similarity

This utility allows searches of databases containing protein, DNA or RNA sequences.

The Sequence Similarity interface is made up of four fields that enable submission and search parameter options. These are:

Below the four fields that provide for sequence submission and data base choice is a Submit button for initiating the sequence search. It normally takes a number of minutes for the sequence search to complete since the query sequence will be compared to all entries in the data base. Progress in the search is indicated by an ongoing report seen below the submission button.

Once the sequence comparison has completed results are presented in a table that includes descriptions of search results and parameters used in the search. In particular, there is a list of sequence ranked by the strength of their similarity to the submitted query, as well as the actual sequence alignments.

HyperBrowser

HyperBrowser is a tool that provides search from the perspective of chromosomal position. In Coremine Medical, the interface is divided below two tabs: Search (the search submission window) and Analyze (becomes populated by the results of a search). The Search pane includes a submission field that allows you to choose from the list of concepts included in Coremine Medical. Your search concepts lists concepts chosen for the search, and Options allows you to choose which genome, etc. you would like to address in the search. Visit the help pages at HyperBrowser to learn more.

File upload

Here you can upload of a tab delimited text file that contains a list of concepts to be explored simultaneously. At present the relevant types of information that can be handled are files that contain lists of gene or protein symbols. Numerical values can also be added to create a data column (e.g. differential expression values from an array experiment) and the file can contain header lines (column labels). File upload allows you to view concepts coupled to these values and to select a subset of concepts to explore. Coremine Medical is currently capable of handling submitted sets of of up to 300 genes or proteins.

File upload and submission of concepts is accomplished in four steps.

  1. Locate and import file
  2. Assign header rows, ID and Value columns and settings appropriate for your list
  3. View table and choose concepts of interest
  4. Submit the data to Coremine Medical Explorer
Find the file you wish to import on your computer using the Browse button and conventional exploration of directories. Click the "Import" button. The file contents will appear in a table. Select the appropriate options for your files: Notice that the table contents and column headings will change depending on which selections you make. Click Reset if you wish to start over.

Once you are satisfied that the options chosen are correct for your data, begin selecting concepts to explore. Notice that you can sort the table by clicking on column headings and that there are paging arrows under the table.

After your selections are complete, click the submit button and the Explorer window will open showing the selected concepts as a concept map.

© PubGene 2014 Disclaimer: Coremine Medical does not provide medical advice. Terms of use