EndNote™ – PDF Harvesting Changes! June 1st is the Drop Dead Date to change!

EndNote Edit Menu - choose Preferences 2017-05-17Many of you use EndNote to harvest or gather PDFs in your EndNote Library.  It’s a huge time saver when you are trying to collect the articles you need for a grant or manuscript. The library has changed how we are able to do this and you need to update your settings as soon as possible. If you don’t make this change, your copy of EndNote will stop harvesting PDFs on June 1st.  Take the time to make this change now, the new URL is already working.

In Endnote, go to the “Edit” drop down menu and choose “Preferences”.

In the EndNote Preferences box, make sure you have “Find Full Text” selected.

EndNote Find-Full-Text-box-2017-05-17

Check all 4 of the checkboxes.  The “OpenURL Path:” field should be

https://primo.hsl.ucdenver.edu/openurl/01UCOHS/01UCOHS?

Copy and paste this into the field or type it very deliberately.  Uppercase matters and must be typed exactly as shown.  Include the “?” at the end.  Please note the URL begins with https.  You only need to fill in the “Authenticate with: URL:” field if you are trying to harvest or gather PDFs when you are not on campus. If you only use EndNote on campus you don’t need to populate this field.  If you are using it, it should be

https://hsl-ezproxy.ucdenver.edu/login

If you need assistance or would like us to help walk you through any of these changes, you can reach the Education & Reference department in the library from 9:00am through 4:00pm at 303-724-2109.

What are your 3 library wishes?

Library Wishes Genie LampIf the Library Genie granted you three library wishes, what would they be?  Now you have the opportunity to let us know!

Submit your three wishes to the library genie today!  Your wishes will be anonymous, but if you’d be willing to talk more with us about your wishes you can include your name and e-mail address.

  • Are there resources or services you’d like to see the library offer?
  • Has the library implemented enhancements that you’d like to see more of?
  • How could the library better assist you with your research, education or clinical needs?

What in the world is ORCiD?

If yorchids-nationalorchidgarden-20041025ou’re thinking that I merely misspelled the name these beautiful flowers,  you’d be mistaken.

ORCiD is a non-profit organization that provides unique identifiers for researchers.

This 16-digit identifier to any research output, such as publications, datasets, posters, basically anything. It’s basically a bar code that you can apply to your work to link you to your accomplishments.

ORCiD is currently being used worldwide. In fact, many publishers and international funding agencies require ORCiD iDs on funding applications and manuscript submissions.

Why are unique identifiers for researchers important?

A major challenge in cataloging research output for individuals and institutions is matching researchers to their output. Currently, the only way we have to distinguish researchers from one another are names and affiliations. This system is problematic for a number of reasons:

  • Names can change over the course of a career. This situation often occurs due to changes in marital status.
  • So do affiliations. Researchers almost certainly change their institution through their MD/PhD and postdoctoral training, but many also have other steps along the way.
  • Names are not unique. Many researchers, even within the same field, have the same or similar names, especially when databases only store first and middle initials.
  • Name formats are often not standardized. Researchers often publish under variations of the same names: some journals include first and middle names, some only accept first, not to mention typos.

To compound this problem, there is no one comprehensive source for all research publications. Thus, automated searches, such as the PubMed search strategy used with Colorado PROFILES, have issues with sensitivity and specificity. Faculty are asked to log in and curate their profiles, but many do not. A widely-used unique identifier for researchers that can travel with a researcher across institutions and can be integrated into many databases would solve this problem.

How does  orcid-logo fit in?

Because ORCiD is an independent non-profit organization, they provide an identifier that can be used for anything, anywhere. It stays with the researcher though name and affiliation changes. Even PubMed has an Author – Identifier field that uses ORCiD iDs now.

How is ORCiD different from other profile systems like ResearchGate and LinkedIn?

ORCiD isn’t meant to replace any of these systems. It’s not a professional networking platform like Research Gate and LinkedIn. ORCiD does provide an online profile system where researchers can display their accomplishments… or not. The ORCiD iD itself is useful even if you never fill out the profile system.  Additionally, these platforms do not provide a unique identifier. In fact, ResearchGate includes a field for ORCiD iD!

How is ORCiD different from other unique IDs for research output like Web of Science Researcher ID and Scopus Author ID?

Researcher ID and Author ID are, as indicated by their names, are unique IDs for researchers. However, their limitation is that they only link to citations within their respective databases (Web of Science and Scopus). Thus, they do not capture the whole picture. ORCiD iDs are platform agnostic and can import data from your Researcher and Author IDs, so you don’t have to start from scratch.

What about Google Scholar Citation Profile?

Google Scholar Citations is designed for you to keep track of your publications and associated citation metrics. ORCiD doesn’t do these things, but Google Scholar does not create a unique identifier.

But I already have all these things set up. Can I import things from these places?

Yes! Here are a list of tutorials:

ORCiD has not formed partnerships with ResearchGate and LinkedIn to allow direct transfer of information. ResearchGate does have a field where you can input your ORCiD iD.

How do I register for an ORCiD iD?

Individuals can get an ORCiD iD for free.

ORCiD has institutional partners that can automate this process for their faculty based on information they have on file. CU Anschutz has access to CU Boulder’s ORCiD membership. If you have questions or comments about the possibility of CU Anschutz using ORCiD, please contact tobin.magle@ucdenver.edu.

  • Tobin Magle, PhD. Bioinformationist.

 

 

Bioinformatics Bites: MedGen

This bioinformatics bite is going to be a little but more clinically oriented:

A patient is presenting with excess blood clotting, which she thinks might be related to “something that runs in her family”. How do I find known diseases and genes (if any) that are associated with that phenotype?

A good place to start to look for information about symptoms and diseases that are related to genetics is MedGen. This database organizes information related to human medical genetics, like symptoms (clinical features), related genes, diseases, or genomic loci.

A perfectly reasonable approach would be to type “clotting” into the MedGen search box. Here’s what those results look like:

clinfeaturestag

There are 94 results, the first of which is a clotting disorder, but one that is associated with too little clotting rather than too much clotting. If you scroll down, you see records that are not actually diseases:

otherconcepts

To find out what type of record you’re looking at, look at the text after concept ID (blue boxes). The screen captures above show a Disease or Syndrome, a Finding, and a Pharmacologic substance. Notice that the diseases has links to other databases (green circle) and the others do not.

So how do we specify that we’re looking for a patient symptom related to a genetic disease? Like all the other NCBI databases, MedGen has field tags.

Here are some useful ones:

  • Clinical Features: short stature[clinical features] – records for diseases that are associated with short stature
  • Related Genes: LMNB1[gene] – diseases associated with this gene
  • Disease name: achrondroplasia[title] – this disease
  • Chromosome: 6[chromosome]- diseases associated with alterations to chromosome 6

Also, if you look back at the first screen shot, you can see a link that says “See MedGen results with clotting as a clinical feature (5)“. MedGen automatically sensed that clotting was a clinical feature, or symptom, and narrowed your results down for you.

Now we’ve narrowed the MedGen results to those that have clotting listed as a clinical feature. If you read the description, you see that Factor V deficiency is the only one associated with excess clotting. The record also shows what gene is associated with this disorder (F5) and links to descriptions from other resources like GeneReviews and OMIM, as well as Professional guidelines and Recent clinical studies.

result page.png

So how do you find out if this is in fact what your patient has? Find out next week!

-C. Tobin Magle, PhD, Biomedical Sciences Research Support Specialist

 

Bioinformatics Bites: GEO2R

This blog series has covered how to use both GEO Datasets (which holds both curated and uncurated datasets) and GEO Profiles (which holds expression profiles for individual genes from curated data sets).

But what if you want to see expression profiles of a gene from an uncharted dataset? That’s where GEO2R comes in. Once you’ve identified a dataset by searching GEO Datasets, you can start using GEO2R in 5 easy steps:

  1. Pick your experiment
  2. Define sample groups
  3. Assign samples to groups
  4. Perform the test
  5. Interpret the results table

Pick your experiment:

You need an accession number to start using GEO 2R. Which one do you use? Let’s use this dataset from Toxoplasma gondii as an example.

search result

This record contains accession numbers (boxed in red) for the series, samples, and platform. GEO2R is looking for the Series Accession number, GSE73177.  Enter this number into the search field in GEO2R, or click the Analyze with GEO2R link (blue arrow):

definte groups

Define sample groups:

This experiment is measuring expression levels in 3 groups (parent strain, knockout strain, and complemented knockout strain**). Thus, we need to create 3 sample groups. To do this, click “Define Groups” link (green circle above.) This action activates a popup that allows you to enter free text to name the groups (red box, wt, ko, and comp in the following example)

define groups 2.png

Assign samples to groups: 

Now you need to tell the program which samples belong to each group by selecting the samples that you want to put into a group, then clicking on the group you want to add them 2 in the Define Groups popup. In the example below, I have selected the complemented knockout samples (highlighted yellow) and will click the “comp” group to add them. After they are added to a group, the corresponding colors change to that of the group and the group column is populated, as in the case of wt and ko in the example. Repeat this process for all of your groups.

assign to group.png

Perform the test:

Get a list of the top 250 differentially expressed genes using the default settings*, scroll down and click the Top 250 button under the GEO2R tab.

A table containing the top 250 differentially expressed probes from the platform that the probe ID, p-value, adjusted p-value, F statistic and probe sequence.

Interpret the results table:

Clicking on the probe ID will show you a graph of the gene expression among the groups you have specified. You can also click Sample Values to get the number values represented on this graph.

top250

In this case, it looks like the gene that is probed by 55.m10280_at is highly expressed in the knockout relative to the wild type, but doesn’t revert to wild type levels in the complemented strain.

To determine the gene name of the probe used in this experiment, visit the corresponding platform record for this series. (You can find this by searching the Series accession in GEO datasets, and using the platform filter.) Then, scroll to the bottom of the page to see the platform data table, which gives probe IDs, identifiers for genes in the toxoplasma genome database, annotation,chromosome location and a description of the gene function if available. Search for the probe id in the table to find the corresponding gene. In this case, it’s a thioredoxin domain-containing protein.

But what if your gene of interest is not in the top 250? You can use the Profile Graph tab to search by probe id.

GEO2R also has basic QC tools. You can see the value distributions across samples to identify large scale problems in the dataset using the value distribution tab:

value distribution.png

Finally, you can retrieve the R script for the analyses run in the R script tab.

NCBI also has a comprehensive tutorial on this tool if you’re interested.

Let me know if you have any questions!

  • C. Tobin Magle, PhD, Biomedical Science Research Support Specialist

* For novice users, the default settings are a good place to start. The calculation uses the limma package, and you can view and change the default settings by clicking the Options tab.

options tab

** knocked out gene added back in to account for off target effects of the knockout.

New Resource: Quetzal Advanced Version

Quetzal

The library now has access to the Advanced Version of Quetzal! Find it on the library’s database page, or follow the links/directions below.

Version descriptions:
Basic (Free) – Enhanced linguistic searching of PubMed documents to find relevant results.
Advanced – Includes patent, full-text searching and AHRQ Treatment Protocols.

Note: When creating a new individual account, users must be on campus, logged in with their PassportID after following the link below (if off campus), or connected by VPN.

For new users:

  1. Go to Quetzal.
  2. Scroll down to the bottom of the page.
  3. You will see the following message:

quetzal
If it doesn’t say “University of Colorado – Anschutz Medical Campus,” you are not on campus and will need to go through your Proxy Server or VPN

  1. Click the registration button at the bottom of the page:

quetzal 2

  1. Fill out the Registration Form.  Our organization should be pre-selected for “University of Colorado – Anschutz Medical Campus”.  If not, please select that from the drop-down list.  [Note: a separate registration is required for each individual user since each user uses their personal space to save searches, get weekly alerts, save results with personal annotations, and participate in private journal clubs.]
  2. Read the Terms of Use and check the box at the bottom of the Registration page.
  3. Click the Continue button.
  4. You should see a message saying “Your user registration was successful. You may Login to Quetzal® Search now.”  [IMPORTANT NOTE: If you see instead a new form that says “Choose your Subscription type”, then STOP.  You have not been correctly recognized as being from University of Colorado – Anschutz Medical Campus.  Be sure you are on site or logged in through your organization’s Proxy Server.  Or, make sure you are signing up for Quetzal® Advanced, not Professional.]
  5. Happy Searching!  You can follow along with the Guided Tour on your first visit. This will help you understand how to use Quetzal® effectively. You can also check out the information and 30” videos shown in the Quetzal® Quick Help section on the home page (after logging in).
  6. Any questions or problems?  Contact Quertle at info@quertle.com.

For users with an existing Quetzal® Basic account:

  1. Go to Quetzal.
  2. Login to your existing account.
  3. In the upper right corner of the search area, click on “Your Quetzal”.
  4. Click on the My Profile tab. In the Organization drop-down list, be sure our subscribing organization name (University of Colorado – Anschutz Medical Campus ) is chosen.  This should be the same name you see on the Quetzal welcome page in the “Happy News” message at the bottom of the page.  If it is not the same, please select the correct Organization from the list.
  5. Click on the My Account tab.  You should see a Happy News message.  [NOTE: If you do not see the Happy News message, then STOP.  You have not been correctly recognized as being from University of Colorado – Anschutz Medical Campus.  Be sure you are on campus or logged in through your organization’s Proxy Server.]
  6. Click “Change” on the Your Version line.
  7. Choose “Advanced” in the dialog that opens and then click Submit. You may need to log in again.
  8. On your My Account page, the line for “Your Version” should now display Quetzal® Advanced.
  9. Enjoy searching all the content Quetzal® has to offer and the full set of features and functions.
  10. Any questions or problems?  Contact Quertle at info@quertle.com.

Non-AMC campus members can still register for access to the Basic (free) versionhttps://www.quetzal-search.info/