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 discussion groups on a relevant theme. By becoming a registered user of Coremine Medical you can use these tools to explore, exchange information and learn.
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.
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).
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).
The register link opens a dialog box that allows you to become a user of Coremine Medical features such as My Page and Groups. 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.
Opens these help pages.
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:
Opens a page that welcomes you to submit comments and questions regarding Coremine Medical.
Displays hyperlinks to web pages of selected Partners and Supporters of the Coremine Medical project.
Links to pages containing collections of Coremine Medical functions are visible at the upper right of any page in the interface:
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:
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).
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.
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.
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.
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:
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).
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).
Choices under this menu allow you to modify views of the network.
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.
When the image is in Grid view, clicking the Network view button under the Network tools menu returns the presentation to network form.
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.
Allows search for a concept within the network based on the spelling of that concept.
The slider bar adjusts which connected concepts are visible in the network based on the statistical significance of their connection.
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.
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.
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.
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.
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:
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.
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.
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 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.
Removes the node (or all selected nodes).
Opens a new search with the selected concepts, replacing the current network with the results of the new search.
Bookmarking a concept helps you find this concept again in the future. Bookmarks are stored in a table under My Page, Bookmarks.
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.
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.
Here a new search will be launched and a network created that includes concepts associated with either of the connected 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.
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.
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.
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 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.
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.
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 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:
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:
Includes Chemical formula, Category, Type, ATC code, and a list of Brand names.
Describes pathologies that the drug has been approved to treat - that is, the diseases that are normally treated with the drug.
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.
The enzyme or enzymes that degrade the drug molecule (if known). In some cases, drugs are not metabolized but leave the body through urine.
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.
Coremine Medical incorporates some of the links to external references extracted from Drug Bank.
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:
Information shown for Food focus items is that name of the food and synonyms of that name.
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:
Information shown when a concept from the Chemical category is the Focus item is the name of the chemical and synonyms of that name.
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).
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).
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).
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:
Shows a list homologous Gene/proteins identified in other organisms (includes Gene/proteins found in organisms addressed by Coremine Medical).
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.
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.
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:
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.
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.
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.
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.
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.
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:
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.
Lists all MEDLINE (PubMed)articles that include both of the experts among the author list.
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.
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.
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.
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:
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 either Context notes or Groups. Opening the Context notes section shows notes added by other users and also provides a link that will open a form for adding your own note. Opening the Groups section shows groups with which the focus concept has been shared.
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).
Clicking this link shows notes added by users and also shows the link Add context note that opens a new panel with fields for submitting a note.
Notice that notes added by the user appear in the context of the focused element in the network. That is, a note is shown only when its associated node or edge is selected in the concept-map.
You can contribute context notes in two ways; either by adding a new note or commenting on an existing note.
If you wish to contribute a new note, click the "Add a note" button and use the form to submit a context note. Notice that you can either leave notes open to anyone or limit their visibility if you wish: Visible for -
Opening this pane shows the Groups with which the focus concept has been shared.
Only group owners can associate concepts with a group such that these become visible under user updated content. A group owner can share a concept with a group as follows: open Groups Group info and click the Add concept button to open a dialog that will help you find and associate a concept with the group.
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 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.
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:
This tab shows items from your Bookmarks associated with e-mail alerts. Use the "Edit" button to change the parameters and status of alerts.
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 article.
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:
The "Occupation" field contains a list of possible occupations as well as the option to enter "Other".
The Tools page is comprised of the following elements:
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:
In PubMed 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.
Notice also that you can filter by journal name or date range by clicking +Add filter and entering filter criteria in the appropriate fields.
Once you have chosen your desired query concepts and filter criteria you can launch the search by clicking the Submit button.
The List of articles panel will open automatically once a PubMed search has been submitted. The panel contains a table showing a maximum of ten article names at a time. At the top of the panel are the action links First, Previous and Next that allow you to page through the table.
The table is comprised of seven columns:
The abstract for an article appears in the View article pane after having clicked its PMID in the List of articles table.
In addition to the abstract text, View article 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 article are
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.
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:
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:
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.
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.