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Faculty Research Profiles

Collexis Faculty Research Profiles for Wayne State University and Henry Ford Health System

What are Research Profiles? The Department of Clinical and Translational Science (DCaTS) is excited to launch a new tool to help faculty members and departments to identify who is working in what scientific life sciences areas at Wayne State University, Michigan State University, Van Andel Institute, Karmanos and Henry Ford Health System. (HFHS) This tool, powered by Collexis™, is called Faculty Research Profiles and is available at: http://www.researchprofiles.collexis.com/wayne/.

Who Knows What at DCaTS? A consolidated, thorough directory of DCaTS’s life sciences research expertise has not been available to our researchers. An understanding of “who” in the organization is working on “what” can facilitate building collaborative teams and productive research relationships.

What do I use it for? Collexis Faculty Research Profiles contains both career-long and current research information, requires little to no effort for creation or maintenance and is easy to use. We have partnered with Collexis™ to implement the Faculty Research Profiles. In addition to highlighting individual research expertise, the Faculty Research Profiles tool exposes connections among Wayne State University and HFHS researchers and can assist in identifying potential collaborators both internally and at other organizations. This tool can also help find mentors and key knowledge holders, making connections between faculty, students, and staff easier.

What data is included? Collexis' Research Profiles use the freely available MEDLINE publication data (PubMed) as well as NIH-funded grant information (NIH RePORTER) to create a “fingerprint” of a researcher's subject expertise. This fingerprint is updated weekly automatically as publications enter the MEDLINE database, meaning researchers are not required to manually maintain their individual profiles.

How does it fit DCaTS? In order to customize this tool, Collexis was provided with the department structure and mapped researchers to their department or unit. This allows users to browse researchers by department, search by name, or search by topic to find experts in a particular area.

Which researchers are included in the tool? The Faculty Research Profiles tool is intended to highlight our research prominence and, therefore, currently includes a select group of about 700 researchers at Wayne State University and about 200 HFHS researchers that are shown to be working in a life sciences or biomedical research area. The included faculty list is maintained internally, and there may be a lag between a faculty member's hire date and generation of a fingerprint.

We welcome your input to make the Faculty Research Profiles tool as complete and accurate as possible. If you have any questions or concerns, please contact us at MACTS@wayne.edu.

http://www.researchprofiles.collexis.com/wayne/

Description of the Interface and Functions of the Research Profiles Application

This document is organized to help orient users to the user interface and user experience of the tool. Other educational documents present information in a ‘how-to’ manner, or a detailed screen by screen introduction. This one instead takes the approach of introducing the philosophy of the structure of the application and how the different sections are connected through related concepts or through searching.

4 Layers of Detail

There are four main layers throughout the application, each described in general in this document.

  • Home page – Organization overview
  • Department/Unit View
  • Individual Researcher
  • Publication/Grant View – Scientific Context

Each view within the Research Profiles uses all of the information beneath it to create a ‘view’ of information. If looking at the top level it shows information from all departments, all faculty and all publications and grants. If viewing at an individual researcher layer it shows just information about that individual, their own publications and grants and only shows connections with the other elements (peers and departmental information).

Home page – Organization overview

The homepage of the Research Profiles application shows the information that applies to the entire organization begin profiled. Along with the Departmental structure of the organization, it shows a feed of the most recent PubMed publications and NIH-funded grants updated weekly along with a listing of the top journals that the institution publishes in. These links, as well as the search box and search options in the upper right hand corner, provide the main access points to the application. By either clicking a department, publication or grant, or by searching for a concept or person, the user can enter and begin to explore the information presented through exploration.

Department/Unit View

To view research profiles of different faculty departments, browse to the name of the department or division from the alphabetical list, and click. The results page gives you several different options: you can view a research profile of the entire department or view the research profile of individual faculty within the department. There are also many other ways to view the information about the department given all that we know from the documents that have been associated with the researchers in that unit. Once we know all of the co-authors of the unit researchers, we can start to draw inferences about the research network within that group.

To explore these topics, click on an item from the lefthand menu to view information about the department as a whole, including a department research profile, the NIH-funded grants and PubMed publications associated with that department, and representations of collaborative networks and research trends.

The main portion of the window gives you a brief snapshot of some of the data contained in the department overview. You can view the most significant Medical Subject Heading (MeSH) concepts associated with the department, citation information for recent PubMed publications and NIH-funded grant awards, and collaborations within the organization and with other institutions.

To return to the Research Profiles homepage, and see the department list again, click Home in the upper lefthand corner of the page. You can also start a new search from a department profile page by selecting concept, name or fulltext in the upper right hand corner and entering your search terms.

Individual Researcher

To view the research profile of an individual faculty member, just click their name in the alphabetical list on the department home page or search for them by last name. The first item you see is the general profile page – a snapshot of all of the information contained in this person’s research profile. From here, you can view concepts where that researcher is identified as a person with expertise, look at their PubMed publications and NIH-funded grants, and see other researchers they’ve collaborated with.

The menu on the left side allows you to explore each of these sections in more detail, including their publication lists, co-author relationships, other institutions the individual has worked with and even similar experts within the organization.

Publication/Grant View - Scientific Context

The most focused layer of information within the Research Profiles involves drilling all the way down to clicking on an individual PubMed publication or NIH-funded grant. This can be accessed from nearly anywhere in the application – from an individual researcher’s profile, from a department’s list of publications, as a search result, etc. When clicking on a PubMed publication or NIH-funded grant, the Research Profiles tool attempts to make the scientific context of that publication visible. This layer shows information about what is covered in this publication as well as related publications, provides connections to the researchers on that publication or the PubMed entry itself and connects you to other experts, PubMed publications or NIH-funded grants that match this scientific area. This detail is what connects all other information throughout the interface. (Note that if you see no data on the scientific context of a PubMed publication or NIH-funded grant it means that it was just recently added and the development and indexing of the information is still underway.)

Additional Tools and Functionality: Searching

Search by faculty member

Use the search feature of the Research Profile tool to quickly locate the research profile of an individual faculty member. Click on 'By Last Name' under the white search box in the upper righthand corner, and type the last name of the researcher you're searching for. Don't worry about the first name - the system only searches by last name. Once you've typed in the last name of the faculty member, the search results for all matches will be shown, including information about their publication and grant volume and a trendline of their last 10 years of publications. A word of warning – if you spell the last name incorrectly the researcher won’t be found, so if you're not seeing the results you expect, check the spelling of the last name and try again or just put in a portion of the last name (ie, ‘wool’ will return both ‘Woolliscroft’ and ‘Woolford’).

When you click on the name in the search results, you'll be taken directly to that individual's research profile. There's a lot of information on this page, from lists of publications and grants to information about research collaborations both within and outside the institution. The researcher profile page is like a dashboard - you can link into full details of all of the different areas by selecting that topic from the menu on the lefthand side of the page, or by clicking the 'more' link next to each topic. For example, to see the full list of a researcher’s publications, click more. Click the title of an article to see the publication details, including a link to the PubMed record. To move back to the research profile, just use your browser's back button or click the researcher’s name in the upper left. To navigate directly to a specific topic, click it in the menu on the left.

For more information on the networks and trends features, you can view the Research Profiles - Networks and Trends tutorial from the Training Resources page.

To return to the Research Profiles tool homepage, click Home in the upper lefthand corner of the page. You can also start a new search from a research profile page by selecting concept, name or fulltext in the upper right hand corner and entering your search terms.

Search by concept

Use the concept search feature of the Research Profile tool to quickly locate faculty members with research experience in this area. Type the concept you're interested in in the white search box in the upper righthand corner.

The concepts are based on the Medical Subject Headings, or MeSH terms. The Medical Subject Headings are a controlled vocabulary developed and maintained by the National Library of Medicine, and are used to index articles in PubMed/MEDLINE. Each concept in the Research Profiles represents a MeSH term that was associated with a publication by a faculty member.

The length of the bars in the results are indicative of how prevalent the concept is in relation to the other concepts on the page as well as that concept in relation to anyone coded with that term. If a concept has a significantly larger bar than others, it is more unique in relation to that individual and the rest of the organization than a smaller bar. The relative sizing is used to indicate the degree of significance – a big difference in length equals a big difference in significance.

The search engine in the Research Profiles tool has been optimized to work with the MeSH terms, so if you know the MeSH term for your concept, entering that will target your results. Entering a more general term will give you a broader range of related concepts. For example, if you are interested in the concept of breast cancer, typing the MeSH term "breast neoplasms" gives you two results: breast neoplasms, or the more specific male breast neoplasms. Contrast this with your result set if you type breast cancer. While the search does retrieve the concept breast neoplasms, it also brings back related proteins. To learn more about MeSH, you can view the Medical Subject Headings tutorial in the Training Resources section.

To find researchers whose research profiles emphasize breast neoplasms, enter the MeSH term breast neoplasms into the search box. (As an example, if you were to search for breast cancer the interface correctly corrects that to the MeSH term breast neoplasm.) The number next to the term represents the number of research that will appear in the concept profile. Click on the name of the desired concept to view the profile.

The default result set displays faculty listed in order of how significant that term is in their profile based on PubMed publications. If you're interested in relevance based on NIH grant awards, you can change this using the dropdown menu under the experts based on heading.

You can do a few different things from this page: view PubMed publications, link to a faculty research profile, or refine your search by adding related concepts:

  • To view the PubMed publications that include your concept and are associated with a particular faculty member, click the plus sign next to the researcher's name. This shows ‘why’ this person appears in this view and what of their publications best match this term. You can view publication details, including the article's abstract and a link to the PubMed record, by clicking on the article's title. To collapse the article list, click the minus sign.
  • To link to a faculty research profile, click the researcher's name. You can return to this result set from a researcher's profile by using your browser's back button.
  • To refine your search by adding concepts, select the terms from the list on the righthand side of the page. This list is a set of terms that also appear in the publications associated with your search term, and allow you to narrow down your results. Selection options will vary based on your original query, but all of the listed concepts represent MeSH terms that are related to your original query in faculty publications. For example, to find researchers who have published on breast neoplasms AND tamoxifen, click the Add button next to tamoxifen. Your result set narrows. Notice that your search parameters are displayed, and you can continue to refine your search. To remove a concept from your search, just click the Remove button next to that concept.

To return to the Research Profiles homepage, click Home in the upper lefthand corner of the page. You can also start a new search from a concept results page by selecting concept, name or fulltext in the upper right hand corner and entering your search terms.

If you have any questions about how to use the Research Profiles tool, please send an email to: MACTS@wayne.edu. We welcome your questions, comments and suggestions!

Search by Full-text

The fulltext search is a great way to find faculty with related expertise. You can copy and paste full-text from any source, such as an article, grant abstracts, publication or funding announcement to quickly find researchers with expertise in an area.

To use the fulltext search feature, first copy text from a source page or document. Alternatively, you can type in any set of activities or descriptions you may want – any text that gets entered can be analyzed and searched. In this example, we'll use the abstract from a PubMed record. Copy as much of the fulltext as you'd like, then return to the Collexis Research Profile tool. Under the white search box, click "by fulltext". Paste the text you've just copied into the search box and click 'Find'.

The results screen will display up to 50 researchers, listed in order of relevance to the text you're searching against. From the results screen, you have a few different options. Of course, you can click on the name of an individual faculty member to go directly to that research profile. You can also choose to view faculty expertise by NIH-funded grants rather than PubMed publications, which is the default search. Notice that this changes the faculty profile list considerably. You can also use the terms under the Fingerprint heading to refine your search by moving the button to the left or right to decrease or increase the significance of that concept in your search and selecting one of the four Ratings Weights: Low, Medium, High or Required. For example, by requiring that specific concepts appear in the profiles of all faculty members in my results set, you may take the list of returned researchers from 50 down to 10.

Changing the amount of text pasted into the box can also affect the result set. You can delete text from the search box and view how this changes your search. If you want to return to your original fulltext search, just paste it in again.

To return to the Research Profiles homepage, click Home in the upper lefthand corner of the page. You can also start a new search from this results page by selecting concept, name or fulltext under the search box and entering your desired term.

If you have any questions about how to use the Research Profiles tool, please send an email to: MACTS@wayne.edu We welcome your questions, comments and suggestions!

General FAQs

Who can access the DCaTS Research Profiles?

Anyone who has the tool URL (http://www.researchprofiles.collexis.com/wayne) can view the DCaTS Research Profiles. This enables funding agencies, corporate sponsors, patients and interested parties to gain more access to the DCaTS research consortium.

What are Medical Subject Headings (MeSH terms)

The Medical Subject Headings (MeSH®) thesaurus is a controlled vocabulary produced by the National Library of Medicine and used for indexing, cataloging, and searching for biomedical and health-related information and documents.

2010 MeSH includes the subject descriptors appearing in MEDLINE®/PubMed®, the NLM catalog database, and other NLM databases.

Many synonyms, near-synonyms, and closely related concepts are included as entry terms to help users find the most relevant MeSH descriptor for the concept they are seeking. In NLM's online databases, many terms entered by searchers are automatically mapped to MeSH descriptors to facilitate retrieval of relevant information.

Various online systems provide access to MeSH and the vocabulary is available in several online systems. These include the MeSH Browser, containing the complete contents of the vocabulary; the MeSH Entrez databases, which are designed to assist those searching MEDLINE/PubMed; and the UMLS Metathesaurus® with links to many other controlled vocabularies. Additional information about MeSH and direct access to MeSH data is provided on the Web at http://www.nlm.nih.gov/mesh.

What grants are included?

The grant data included in the interface comes from the NIH ExPORTER system. New grants appear in this list weekly. Previous years may be selected using the dropdown menu. The source of grants for this application is NIH ExPORTER, so only NIH grants are included. Note that ExPORTER is currently in a beta version until October 1, 2010, and therefore some data may not match the NIH RePORTER interface. More information is available at: http://projectreporter.nih.gov/ExPORTER/ExPORTER_Catalog.aspx.

What is PubMed/MedLine? What publications are included?

PubMed (http://www.ncbi.nlm.nih.gov/pubmed/) lets you search millions of journal citations and abstracts in the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and preclinical sciences. It includes access to MEDLINE® and to citations for selected articles in life science journals not included in MEDLINE. PubMed also provides access to additional relevant Web sites and links to the other National Center for Biotechnology Information (NCBI) molecular biology resources. http://www.ncbi.nlm.nih.gov/

PubMed is a free resource that is developed and maintained by the National Center for Biotechnology Information (NCBI), at the U.S. National Library of Medicine (NLM), located at the National Institutes of Health (NIH).

What publications are NOT included?

Articles that have been published in journals not included in PubMed will not show up in the Collexis interface. For a complete listing of journals covered by PubMed see: http://www.ncbi.nlm.nih.gov/entrez/citmatch_help.html#JournalLists

Why does the research visualization move?

The research visualization we have created is a force directed visualization and is constantly re-evaluating the information that is presented to try to make all lines as equal a length as possible with as few crossing lines as possible. Because there is so much information trying to fit into the screen, it constantly re-evaluates and moves the visualization. It also rotates the visualization in three dimensions to expose other areas of the visualization in a 2D environment. At any time, clicking on any node or line, or clicking the pause button at the top right, will stop this motion so the user can explore the details easier by clicking and dragging the nodes around.

What is the relationship between Medical Subject Headings (MeSH terms) and the Research Profile concepts I see?

The full MeSH ontology is far too complex to put in the interface in any format that is approachable, so we have boiled the MeSH ontology down to a set of research terms that are much more navigable. We’ve done this by reducing the redundancy and detail layers of the MeSH term, resulting in a listing of information that is more navigable by the average user. Collexis does update the MeSH terms on a annual basis to ensure it is in sync with controlled vocabulary.

Why don’t the [+] boxes appear on the ‘Full Text’ search?

One of the features that is standard throughout the interface is that an accordion box [+] appears next to terms to explore ‘why’ that term is appearing. When searching for experts related to a specific term, the [+] box will allow you to see what publications cause that term to appear associated with that expert. These publications appear in order of how significant the publication is related to the term that has been searched for. In order to make the full text weighting work in the results retuned by full text search, we remove this [+] feature in the interface.

Which researchers are included in the tool?

The Faculty Research Profiles tool is intended to highlight our research prominence and, therefore, currently includes a select group of about 700 researchers at Wayne State University and about 200 HFHS researchers that are shown to be working in a life sciences or biomedical research area. The included faculty list is maintained internally, and there may be a lag between a faculty member's hire date and generation of a fingerprint. For a current list of the faculty contact MACTS@wayne.edu.

How can I add my name to the faculty list to be included the DCaTS Research Profiles?

Contact MACTS@wayne.edu, if you are interested in being included in the DCaTS Research Profiles.

How often is the DCaTS Faculty Research Profiles updated?

The faculty research profiles are updated on a weekly basis over the weekend and thus on Monday morning each week it has been refreshed with the most current PubMed publications and NIH-funded grants.

What is the difference between a researcher’s BioMedExpert Profile and the DCaTS profile? How are they similar or different?

The BioMedExpert profile uses only a basic algorithm to assign concepts from their disambiguated information. When an expert is included in a Research Profiles implementation, their fingerprint is more refined and finely detailed as compared to BME. Can a faculty member provide someone his or her DCaTS profile URL? Will that link remain the same after the database is refreshed? Yes, a faculty member can provide someone his or her DCaTS profile URL, simply by copying and pasting it into an email or document. The URl does not change after the weekly database refresh.

What other Universities are using the Research Profiles? Can others access them too?

See: http://www.collexis.com/products/expertprofiling.htm

Who is Collexis?

Collexis Holdings Inc., a leading developer of semantic search and knowledge discovery software since 1999, is headquartered in Columbia, South Carolina (USA) with major operations in; Geldermalsen, The Netherlands; Cologne, Germany and Valparaiso, Chile. Collexis patented technology builds conceptual profiles of text, called Fingerprints, from documents, websites, e-mails and other digitized content and matches them with a comprehensive list of pre-defined “fingerprinted” concepts to make research results more relevant and efficient. This concept matching eliminates the ambiguity and lack of priority associated with word searches. Users often describe the results as finding the proverbial needle in many haystacks. Through this innovative approach, Collexis can build unique applications to search, index, and aggregate information as well as prioritize, trend, and predict data based on sources in multiple industries without the limitations of language or dialect. Representative clients include the National Institutes of Health , Johns Hopkins University, the Univeristy of Miami and the University of Michigan, to name a few. Thanks to our international scientific backgrounds, global management experience, and strong customer support teams, we have the in-depth knowledge and understanding of the requirements for our own and related technologies, and we encourage you to explore our Industry Solutions section for more information on how Collexis can help in your success.

Our Mission: Through conceptualization, our software enables discovery by aggregating and analyzing relevant information far beyond any other technology.

If I find an error in my profile, how do I get it corrected? Collexis maintains a full team of Quality Assurance (QA) professionals that validate the disambiguation algorithm is working correctly, and each user can adjust their content by emailing this QA team at perfectprofiles@collexis.com, a link that is available on each researcher’s individual profile page within the application.

Who can I contact for help or to provide a demo of Research Profiles?

DCaTS librarians are available to support the Faculty Research Profiles, as well as general DCaTS staff. Please contact one of the following:

General
  Kathy Beard
    313-993-4539
    MACTS@wayne.edu

Tutorial/Help
    School of Medicine
      Deborah Charbaneau
      313-577-9593
      dcharbon@med.wayne.edu
    Eugene Applebaum College of Pharmacy and Health Sciences
       Wendy Wu
       313-577-0586
       wendywu@med.wayne.edu
    WSU Main Campus
        Annette Healy 
        313-577-5103
        ak2203@wayne.edu 
    Jon McGlone 
        313-577-6294
        jwmcglone@wayne.edu 
    Henry Ford Health System
        Gayle  Williams 
        313-916-2550
        gwillia3@hfhs.org

How do I use the Faculty Research Profiles?

There are many different uses for the Collexis' Research Profiles, some of which are outlined below. Please review the sample use cases as a starting point for using the tool:

  1. Find a faculty expert on a specific topic
  2. Find out what a Researcher expert is doing
  3. Find PubMed publications by a Researcher expert
  4. Find out what topics Faculty experts are NIH-funded to work on [sentence structure]
  5. Find matching researchers to a funding announcement or research description

I. Find a faculty expert on a specific topic:

Starting at the Home page: http://www.researchprofiles.collexis.com/wayne/

  1. At the upper right hand corner of the screen, in the text box with 'By Concept' highlighted, enter the topic for which you want to find an expert.
  2. The search tool will automatically translate your "search term" into a matching MeSH term(s).
  3. If presented a list of MeSH terms, click on the MeSH term that most closely matches the search term (i.e., the concept of interest to you).
  4. The term you are searching for shows up in the upper right hand corner, noting you may select the source of the results to be publications or grants.
  5. The left column will list the Faculty experts in order of significance and uniqueness to the topic you are searching. You can click the [+] next to each expert to see the publications or grants that cause them to show up associated with that topic.
  6. The right column shows additional concepts that overlapped in publications with the term you are viewing. You can refine your query by clicking “Add” next to the term. This will allow you to narrow your search, giving you more specific results. You may add and remove concepts, refreshing the matching experts on the left.
  7. Click on one of the faculty experts to view their profile, including details on their publications and grants.

II. Find out what a researcher is doing:

Starting at the Home page: http://www.researchprofiles.collexis.com/wayne/

Searching:
  1. In the upper right hand corner, select ‘By Last Name’ and enter a search for a researcher’s last name. You may enter just a few letters of their last name to return more results.
  2. Click on one of the faculty experts to view their profile, including details on their publications and grants, co-authors, institutional connections and their research network.
Browsing:
  1. Navigate using the department structure to find experts and profiles of full departments
  2. Click on a department to see a list of faculty with primary appointments in that department and the research profile of that department.
  3. Click on one of the faculty experts to view their profile, including details on their publications and grants, co-authors, institutional connections and their research network.

III. Find publications by a Researcher expert:

Starting at the Home page: http://www.researchprofiles.collexis.com/wayne/

Searching
  1. In the upper right hand corner, select ‘By Last Name’ and enter a search for a researcher’s last name. You may enter just a few letters of their last name to return more results.
  2. Choose the ‘Publications’ item on the left side to see a chronological listing of their publications.
  3. Clicking on each publication provides more information on the publication and related topics.
Browsing
  1. Navigate through the department structure by clicking on the Department name and then locating faculty in the alphabetical list of faculty.
  2. Click on one of the faculty experts to view their profile, including details on their publications and grants, co-authors and more.
  3. Click on the "Publications" item on the left to view publications.

IV. Find grant awards for a Researcher expert:

Starting at the Home page: http://www.researchprofiles.collexis.com/wayne/

  1. In the text box next to "by last name," enter the last name of a Researcher; or, navigate to the researcher through the department structure.
  2. Click on one of the faculty experts to view their profile.
  3. Click on the Grants menu item on the left to view active NIH-funded grants for the researcher.

V. Finding researchers who match a funding announcement or research description:

Starting at the Home page: http://www.researchprofiles.collexis.com/wayne/

  1. In the upper right hand corner, choose ‘Full Text’ for the search option.
  2. Paste into the text box any free text you would like and click ‘Find’. For example, enter the research objectives section of a funding announcement.
  3. The recommended fingerprint will be created on the right hand side, with recommended weights for each research term. The researchers inside the institution that match this fingerprint are returned in order on the left hand side.
  4. Adjust the weights, or remove concepts, to create a more appropriate fingerprint if necessary. Each change in weighting will adjust the search results and refresh the list of experts on the left side of the page.
  5. Click the researcher’s name to see more information on their activities and academic output. In short, when using the Full Text search you can get a quick list of the experts, but to see the relevant publications you need to drill down on an author's profile listings. The profile list may not contain the exact term you used in the search. And, this will list publications where they are not the first author, but may be a co-author.