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Frequently Asked Questions

ModelMatcher is a global registry and search tool that is designed to facilitate collaborations between scientists and other stake holders of rare and undiagnosed disease research. While the primary goal of this project is to stimulate interactions between clinicians and basic scientists who are interested in the same/homologous genes, ModelMatcher can be used by patients, family members, funding agencies and industry. Our goal is to bring these communities together to facilitate mutually beneficial collaborative projects that advance scientific knowledge and patient care.

ModelMatcher is being developed by a group of scientists, clinicians and bioinformaticians who work at the Jan & Dan Duncan Neurological Research Institute at Texas Children’s Hospital and at Baylor College of Medicine. This team at the Texas Medical Center are working closely with the team developing the Rare Diseases Models & Mechanisms Network software at University of British Columbia. The Rare Diseases: Models and Mechanics (RDMM) software is open source and available at GitHub. You can learn more about the individual members on the “About Us” link at the top of the page.

Scientists register their human or model organism genes of interest in the "Scientist Registry". users who wish to connect with these Scientists register their human genes of interest in the "Match Dashboard". ModelMatcher then generates a table in the Match Dashboard showing all the Scientists who share a gene of interest with them. The users are able to send official Match Requests to each Scientists via the Match Dashboard. The Match Dashboard will also keep track of when the last message was sent, and will notify registered users if a new Scientist registers a shared gene of interest in a future timepoint. The Scientist can then respond to the Match Request by contacting the Match Dashboard user through email.

Both the Scientist Registry and Match Dashboard pages of ModelMatcher are password-protected and the information you enter will be kept secure. The visibility of your information depends on your Data Privacy setting for each gene you select. The management team of the ModelMatcher project will have access to all data for administrative purposes.

The profile information a Scientist enters in the Scientist Registry is made public, and can be accessed through both the "Search" and "Match" feature of ModelMatcher and partner registries. The visibility of your genes of interest can be optimized using your Data Privacy setting for each gene you select.

  • Public - Your information will be visible publicly. Anyone can obtain information on these genes through ModelMatcher’s public search webpage. This information will also be shared with our partner model organism registries including RDMM (Canada)Solve-RD (Europe) and AFGN (Australia).
  • Restricted - A subset of genes of expertise/interest that can only be discovered by ModelMatcher users using the Match Dashboard feature, which requires the user to register with ModelMatcher. These typically include genes in which the Scientist user has unpublished data on and considers confidential.

The information users enters in the Match Dashboard will only be shared with Scientists who you attempt to reach out to using the Match Request feature.

ModelMatcher is connected with model organism researcher registries around the world in order to maximize collaboration efforts. We share data between these registries so people on those systems can find collaborators on our system and vice versa. Currently, we partner with RDMM (Canada)Solve-RD (Europe) and AFGN (Australia), and this list may grow as more and more registries are established with similar goals and virtues.

ModelMatcher will also be connected to clinical registries that are part of the Matchmaker Exchange databases including GeneMatcher, PhenomeCentral and MyGene2 to bridge the basic scientific and clinical communities. If there are other registries that wishes to connect with ModelMatcher, please contact us.

ModelMatcher currently support research conducted on Human, Mouse, Rat, Frog, Zebrafish, Fruit Fly, Nematode Worm, Fission Yeast, Budding Yeast and E. coli genes. Even if a model organism of interest is not supported, Scientists can enter their gene of interest based on the Human homolog and this information will be indicated in the Scientist's Profile page.

You can add any gene that you are interested in establishing a collaboration for. If your lab actively works on a specific gene, you should list it as "Primary (Tier 1) when you add it to your profile. The genes you are interested in but don't actively work on now can be listed as "Secondary (Tier 2)" genes. We recommend Scientists to add most genes as "Public" so you can be discovered through the Search feature of ModelMatcher, but you can also add genes as "Restricted" if you wish to identify collaborators on confidential projects. Match Requests made to you about restricted genes does not reveal your identity to the person performing the Match Request. They will only know who you are if you choose to respond to their message.

  • Public - Your information will be visible publicly. Anyone can obtain information on these genes through ModelMatcher’s public search webpage. Your information will be shared (see above) with registered users and will be accessible to non-registered users through the registry’s public search webpage. This information will also be shared with our partner model organism registries including RDMM (Canada), Solve-RD (Europe), and AFGN (Australia).
  • Restricted - Restricted genes: Genes that are classified as Restricted will only be used to perform matches with registered Match Dashboard users. If Scientists do not wish to publicly disclose that they are interested in certain genes (e.g. unpublished genes with preliminary data, genes in which collaboration is underway with confidentiality), we recommend they classify these genes into the Restricted category.

ModelMatcher has two tiers of gene expertise: those you currently work on, or those you could rapidly position yourself to work on. These are called Primary (Tier 1) or Secondary (Tier 2).
Primary genes (tier 1 genes, genes you currently work on): These are genes which your lab actively works on, and you have most reagents, assays and protocols ready to perform functional assays
Secondary genes (tier 2 genes, genes you currently don't work on): These are genes which your lab has worked on in the past or have strong interest in, but would need additional time to establish protocols or create reagents to perform functional assays

No. When you are adding model organism genes, please use the official gene symbol for the gene you study in that model organism. The only time you would need to identify a human homolog and input that gene is if you work in a model organism not supported by ModelMatcher.

ModelMatcher uses DIOPT to find homologs to human genes. Currently, we use a score > 5 and best score in either forward or reverse as cutoffs for homologous genes. For some species that are not covered by DIOPT (e.g. E. coli) or there are true homologous gene pairs with low DIOPT scores, we try to manually add them to our list of potential ortholog candidates (the taxon and gene ID's in this file are all NCBI format). We are always trying to improve our system, so if you notice a homologous gene is not coming up, or a non-homologous gene is, please reach out to us using the feedback feature. Our team will review the relevant data and change our homolog outputs to increase our accuracy!

The Search page allows you to search Scientists who chose to publicly share their genes of interest. users can also connect to partner registries including RDMM (Canada), Solve-RD (Europe), and AFGN (Australia) and display/search their public information from their Scientists users.

After clicking on the Search button, the list of Scientists and their information summary will be displayed at the bottom of the page. Our partner registries results will be displayed in a separate section. Clicking on the "view user profile" button will open a new tab with the user's full profile and gene information.

Gene symbols are organism-specific and will be matched against the list of known gene symbols for the selected organism (selection made in a dropdown menu). Currently, we use the NCBI Gene symbol for all organisms. As a default, users can enter a human gene symbol and obtain results for all supported model organisms. To learn about how ModelMatcher identifies potential orthologs, please visit the "How does ModelMatcher determine model organism homologs?" FAQ entry.

The Match Dashboard is our registry designed for both non-Scientist users, or Scientists who wish to connect with other Scientists. users of this service will create a profile which includes their name, user type (clinician, patient, non-profit, etc.) and an email address. The user then inputs human genes they are interested in. A table of predicted homologs and the Scientists who work on them is generated from this data. From this table, users can send official Match Requests to each Scientist. This is the only way to reach out to an anonymous Scientist who have registered a gene under the Restricted privacy section. If the scientist wishes to collaborate, they will respond to the email address associated with your Match Dashboard Account. You can also opt in to have ModelMatcher notify you when a new Scientist user registers one of your genes of interest (feature under development).

The Search function is open to anyone, regardless of registration, and shows the genes scientists publicly announce they work on. You can also look at the scientists' profiles to get contact information. The Match Dashboard allows users to register, send official Match Requests, and sign up for notifications if a new scientist registers one of their genes of interest. It is also the only was a user can contact a scientist with a gene under the restricted privacy setting.

If you are using the public search function, you can attempt to contact them with the information listed on their profile. Registered users can initiate a Match Request from their Match Dashboard where they can write a short message about their interest in this gene. ModelMatcher will generate an official email detailing who you are, your interest in the gene, and ways to contact you and send it to the scientist as well as sending you a copy of the message and recording when you last contacted the scientist on your Match Dashboard.

Development and release of ModelMatcher will occur in multiple phases. Phase I is to recruit Scientists to participate in ModelMatcher to generate a sufficiently large registry. Since this is a rolling process, Scientists registered and genes represented, will increase as our userbase grows. Phase 2 is to develop the Match Dashboard feature so users can match with scientists and effectively communicate with them. Phase 3 is to connect ModelMatcher to databases that are part of the Matchmaker Exchange and other federated human databases that are designed to primarily perform matchmaking between Clinicians. Upon development of APIs that allow communication with other databases in a secure fashion, including GeneMatcher, PhenomeCentral and MyGene2. Users will be able to match with Clinicians who are part of these large federated clinical matchmaking databases to identify potential collaborators.

Yes, but there are some rules! Our Model Organism, Model System and Organ System icons are registered under Creative Commons BY-NC 4.0. This means you are free to use them in any non-commercial way as long as you credit ModelMatcher. Image files of each icon used on this website can be found here.

Glossary

Scientists: Users who are scientists with expertise in specific genes who access ModelMatcher. Scientists who register in ModelMatcher are willing to use in vivo, in vitro, and/or in silico methods to experimentally study the function of genes and variants linked to human diseases.

Non-Scientist Users: Users with a clinical interest who access ModelMatcher to identify scientific collaborators. These users may be clinicians (e.g. physicians, genetic counselors) who are trying to diagnose a rare disease patient, patients themselves, or their family members who wish to participate in research to understand the mechanism of their disease. Funding agencies and non-profit organizations can use ModelMatcher as non-scientist Users to identify a group of scientists with expertise in a specific gene to facilitate collaborative research.

Genes of expertise/interest: A list of genes that a Scientist User registers in ModelMatcher as having expertise or interest in.

Public genes: A subset of genes of expertise/interest that can be discovered by non-scientist Users using the “Search” feature, which does not require the user to be logged in or registered with ModelMatcher. These typically include genes in which the Scientist User has published on the past and considers non-confidential.

Restricted genes: A subset of genes of expertise/interest that can only be discovered by Match Dashboard Users using the "Match Request" feature, which requires the user to register with ModelMatcher or other federated matchmaking databases. These typically include genes in which the Scientist User has unpublished data on and considers confidential.

Primary genes (tier 1 genes, genes you currently work on): These are genes which your lab actively works on, and you have the reagents and protocols ready to perform functional assays

Secondary genes (tier 2 genes, genes you currently don’t work on): These are genes which your lab has worked on in the past or have strong interest in, but would need additional time to establish protocols or create reagents to perform functional assays

Match Dashboard: The profile page for users to register their genes of interest who wish to reach out to Scientist Users working on those genes and their predicted homologs. This is the location where ModelMatcher users send "Match Requests", and is the only way to connect with users who have registered a gene under the restricted privacy level.

© 2021 by the ModelMatcher Development Teams.
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