SEARCH TIPS | WHAT IS THIS? (example searches: cerebellum, "pulvinar nucleus", gene:grm1)
The Antibody Registry is primarily a tool geared toward scientists attempting to disambiguate antibody reagents in publications. The data are represented inside of a simple search in the neuroscience information framework and inside of the database for advanced users that wish to annotate and add to the AntibodyRegistry.
Using the simple search:
From the AntibodyRegistry home page, a user can click on the Search Antibodies in NIF (Simple Search) and be taken to the NIF system where a sample query for the gene:Grm1 is filled out.
Here one can use the search box to add to or replace the query. Below, we are replacing the gene:Grm1 to gene:SNCA, our gene of interest. If the query starts with a ‘gene:’ then the drop-down menu shows only gene symbols from NCBI Gene.
The new query brings back 388 genes that match the SNCA query terms and each gene has the associated antibody ID number as well as what should be enough information to disambiguate antibodies.
Advanced use of AntibodyRegistry: Adding antibodies, editing antibodies, annotation
The web form for the AntibodyRegistry is relatively simple, but requires a little training and this tutorial should provide this.
While the web form may look daunting at first, we have highlighted two fields which most users should start with in yellow: the Catalog # and Vendor/Provider. Both fields have an autocomplete feature to help users take advantage of the information inside of the AntibodyRegistry.
When searching all fields, but especially when searching the catalog #, we strongly recommend using the autocomplete feature because any user may be confused by a catalog number that has both numbers and letters. For example, published papers include many forms of what may be the same catalog number, but only one will produce the desired data: MP-111, MP 111 and mp111.
The Vendor/Provider field also has autocomplete from a list of all possible antibody vendors, currently in the registry. Because we allow for anyone to add antibodies, not all antibody providers have only one name, but we continually work to reduce the complexity and correctly attribute antibodies to the appropriate companies.
In most cases, the catalog number is unique enough to reduce the number of possible antibodies two less than 5 and in our experience many of these are the same antibody provided by different companies. In the case that, no catalog number is available it is a good idea to start with the Vendor and narrow down the search successively.
In the above example, Millipore gives us 8000 antibodies, which can be searched further by providing other information into the dark gray boxes. For example, Clone ID, Raised in Species and/or Clonality should reduce the total number of entries to a manageable number. Note, the current system does not autocomplete from the current result set, so if there is a clone ID that is not carried by Millipore, then the AntibodyRegistry will bring back no data. Deleting Millipore will bring back all results that match that clone ID.
The results are displayed on the lower half of the screen and the most important piece of information in the AntibodyRegistry is in the first column, the Antibody ID. Searching through these data is less efficient in this advanced form than in the simple search (described above).
If an undesired set of data is returned, use the Clear Form button to start again.
To register new data, or edit existing records we have to authenticate the user by signing in (look at the top right corner of the form).
Follow the directions in the log in and create new user forms to register. An email will be sent to the address provided, to verify the user name and at that point the user can add, edit and even delete antibodies.
If an antibody is selected by clicking anywhere on the lower portion of the screen then the information for that antibody is filled into the form on top. The edit button also appears on the form instead of the add button.
Typing in any of the fields in the top of the form such as the name of the Vendor, or the catalog number then hitting the Edit button will create another row under the same antibody_ID. In the interface the changes take place immediately, but it may take several weeks to show up in the NIF simple search.
Below find an explanation of all of the fields.
Catalog #: This is a searchable field. Note, catalog numbers vary in how they are represented for example a scientist may mean the same thing by MP-111, MP 111 and MP111, so we strongly recommend using the autocomplete after typing one or two characters.
Vendor/Provider: This is a searchable field where the vendor (Millipore Inc) or author (Joe Smith, Ph.D.; UCSD) who has the antibody is displayed or can be added. For known vendors please use the autocomplete feature where possible to reduce the problem of alternative spellings. In the case that a vendor or provider changes, the user can EDIT (after loging in) the antibody and new vendor information/catalog number should be entered. This antibody will then have two rows with the same unique id.
Antibody Webaddress or providers email address: This is not a searchable field. Clicking the open button opens a new window with the antibody provider’s page. In the case of the individual provider, just copy and paste the email address into your email program.
Clone ID: This is a searchable field, note clone IDs are not unique so several different antibodies may have the same clone ID and not all vendors provide this information.
AB Target: This is not a searchable field. Most antibodies are generated against a known or identified gene or gene product (however this distinction is not made). In this case the word gene should appear in the AB Target Type field. If you are entering an antibody, please add the Official Symbol for a gene from entrez gene. http://www.ncbi.nlm.nih.gov/
AB Target Entrez GID: This is not a searchable field. This field should be filled in with the gene-product Entrez gene ID recognized by the antibody. http://www.ncbi.nlm.nih.gov/ Note, there is a different ID for each species, please chose the one that identifies the gene, and leave blank if this is not known.
Target Subregion: This is not a searchable field. This field denotes the region of the gene product that the antibody recognizes.
Target Modification: This is not a searchable field. This field denotes the antibody product modification recognized by antibody, for example the Serine 235 phosphorylated version of this gene product.
Target Species: The species that the AB Target is derived from. For example, mouse monoclonal antibody against human GRM1 has a target species of human.
Raised in Species: Organism that produces the antibody product when challenged with antigen. For example, mouse monoclonal antibody against human GRM1 was “Raised in Species” mouse.
Product Isotype: This is a searchable field, which includes information about the type of immunoglobulin, for example IgA.
Product Conjugate: This is a searchable field denoting a compound formed by the union of two entities or compounds. For example, fluorescein tags.
AB Target Type: Denotes the type of entity, in most cases gene that is being reported in the remaining fields referring to antibody target.
Product Form: Monoclonal: An antibody produced by clones of cells such as those isolated after hybridization of activated B lymphocytes with neoplastic cells. These hybrids are often referred to as hybridomas. Polyclonal: immunoglobulins, which arise from more than one clone of B-lymphocyte cells. Polyclonal antibodies that are usually present when antisera from a conventional immunization is used. In some cases, the form is not reported and then this field is left blank.
AB Name: This is not a searchable field because it is a highly variable set of data that includes some or many of the other fields, but it is not required.
Bottom only:
Antibody ID: The unique resource identifier, this is what should be included in publications to identify this as THE antibody that is being used!
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