Advantages and Limitations of Antibody Databases

Antibodypedia

Antibodypedia is a database containing data cards with supplier information (e.g., product number, supplier name, host species, clonality, purification process, reactivity, isotype, concentration, storage, validation data), references, user-submitted validation data, and user comments.

Advantages of Antibodypedia

Other than the data cards, antibodypedia has additional resources such as links to protocols from Nature Protocols, lists of common protein families, and links to other protein-relevant resources. It also offers monetary rewards for uploading validation data by users, and the option to report an error.

Room for Improvement in Antibodypedia

Like most of the antibody databases listed here, Antibodypedia is not overly populated; however, more validation data from users, and references should improve this. It would also be helpful to include RRID numbers to encourage their use among scientists in both academia and industry.

Antibody Resource

Antibody Resource is a database that outputs antibody reagent information in a table format. Such information includes supplier name, product number hyperlinked to supplier website, host species, clonality, quantity in micrograms, species reactivity (whether the protein can be detected across different species), and relevant applications (i.e., suitable to Western blot or others)

Advantages of Antibody Resource

Antibody Resource offers additional helpful information on biological pathways, applications, and other media focused on knowledge translation such as podcasts. It also hosts a Comparison Initiative, where viewers can compare commonly used antibodies from most major suppliers. We also found it very useful that it provides a list of related antibodies often used alongside the queried antibody.

Room for Improvement in Antibody Resource

Antibody Resource is also relatively young, less than a decade, and has similar issues as Antibodypedia. Particularly, as other databases, including RRID numbers would be incredibly helpful for the scientific community.

Antibody Registry

Antibody Registry is another database with a table outputting  supplier product number, full antibody name, conjugation state, target antigen and reactivity, host species, clonality, suitable experimental applications, reference PMID numbers, and primary or secondary specification. However, it is the official antibody identification database for the RRID initiative.

Advantages of Antibody Registry

In the Antibody Registry, records are never deleted, which allows for better tracking. It’s also integrated with the Journal of Comparative Neurology.

Room for Improvement in Antibody Registry

The website could be more efficiently curated. There are some linking errors, and repeated entries. Furthermore, more validation data from users, suppliers and publications should help ensure this registry is more comprehensive. Finally, it would be very helpful for the academic community for other sources found in this database to integrate with RRIDs so the scientific community in both industry and academia becomes more standardized in the use of commercial and in-house shared reagents.

CiteAb

CiteAb is a comprehensive database listing data cards with supplier information (e.g., product number, supplier name, host species, clonality, purification process, reactivity, isotype, concentration, storage, validation data), and additional information such as conjugation state, target protein and gene, modifications, primary or secondary specification, references, and user-submitted validation data. CiteAb also lists market information, bridging the gap between industry and academia.

Advantages of CiteAb

The additional information they list is useful for protocol development (e.g. dilutions used for WB applications). They’re also one of the few database websites from the ones listed here that offers additional resources such as dilution calculators. Like Antibodypedia, they welcome users to report an error in validation data, or general information (e.g. discontinued antibody). Moreover, they link to related antibodies and other reagents often used alongside the queried antibody.

Because it lists market information, it is suitable for both academic and industry researchers. This is highlighted in the fact that  they partner with suppliers to offer the option of finding a custom antibody if none are commercially available for the protein of interest, which is the case for any emerging target of interest in research.

Additional advantages are their extensive reference resources, and their non-monetary-based awards to reward researchers and reagent suppliers with great validation records.

Room for Improvement in CiteAb

More validation data from users, suppliers and publications should help ensure CiteAb continues being a comprehensive resource.

Antibodies Chemically Defined (ABCD)

ABCD was developed by the Geneva Antibody Facility at the University of Geneva, in collaboration with the CALIPHO and Swiss-Prot groups at SIB Swiss Institute of Bioinformatics. They output data cards linking out PMID and doi addresses for publications, with the goal of promoting recombinant antibody production.

Advantages of Antibodies Chemically Defined

They include a FAQ sheet on how to access the FASTA sequence and pdbs associated with the publications they post. Furthermore, they list cross-references to IMGT database links. It is the only database of all listed here that includes actual sequence information on the antibodies in question.

Room for Improvement in Antibodies Chemically Defined

Like the other databases, more validation data from users, suppliers and publications will ensure this database continues to be topnotch. The latter should also include the addition of RRID numbers.

The site is not as user friendly since lack of integration means the user has to dig through other links for the FASTA sequence and pdb.

BenchSci

BenchSci is a machine learning-powered reagent platform that interconnects publications with reagents and makes recommendations for additional experiments based on your searches

Advantages of BenchSci

BenchSci is an incredibly comprehensive resource for reagents not just antibodies. It’s really user friendly, and academic groups can register for free. The output can cluster based on target proteins, or specific antibody names or catalogue numbers. The platform offers publication links, supplier validation data, and independent research groups’ validation experiments, specifically pinpoint the figures in which the antibody was used, as well as data on reactivity, clonality, host, PTMs, conjugation, and specificity. You may also search antibodies for the type of technique, tissue, cell line, and disease, and save search results to get notifications when changes to the antibody happen (e.g. discontinued, or recalls). BenchSci, for the most part, includes RRIDs, and user reviews.

Room for Improvement in Antibody Resource

Of all the databases, BenchSci is perhaps the most comprehensive; however, more engagement from the scientific community is needed in the form of additional user validation data. Holding competitions or other incentives would promote this.

Linscott’s Directory of Immunological & Biological Reagents

Linscott’s Directory of Immunological & Biological Reagents is another repository listing data cards with supplier information (e.g., product number, supplier name, host species, clonality, purification process, isotype, subclass, concentration, storage, target protein, and supplier website).

Advantages of Linscott’s Directory of Immunological & Biological Reagents

What’s interesting about Linscott’s Directory of Immunological & Biological Reagents is that it includes links to review databases (Antybuddy and pAbmAbs).

Room for Improvement in Linscott’s Directory of Immunological & Biological Reagents

It’s great to see additional integration to other reviewer databases; including RRID numbers would also be helpful.

Validated Antibody Database

Validated Antibody Database also lists data cards with supplier information (e.g., product number, supplier name, host species, clonality, purification process, isotype, concentration, storage, shipping conditions, target protein, applications and supplier website). It also includes publications.

Advantages of Validated Antibody Database

Like Linscott’s, it’s a very comprehensive list of reagents, not just antibodies.

Room for Improvement in Validated Antibody Database

It’s not as integrated as other platforms (e.g.“Browse more products” tool does not consistently provide related products). Including RRID numbers would be helpful.

EuroMAbNet

EuroMAbNet also displays data cards, but what’s really cool about it is that unlike the other databases listed here, it catalogues in-house (non-commercial) generated antibodies. It denotes whether they’ve been validated via cross-referencing in the literature ((e.g., host species, clonality, purification process, isotype, subclass, storage, concentration, target protein, applications, cross-reactivity, and lab website).

Advantages of EuroMAbNet

This database certainly needs a spotlight because it allows for lab-to-lab knowledge dissemination and data validation. Furthermore, it provides papers and figures showing how the antibody was used, information on protein localization, and protocols for validation and antibody use.

Room for Improvement in EuroMAbNet

It’s such a great initiative that it would be much more comprehensive by including RRID numbers. Because this is a recent effort, it’s not as comprehensive, particularly because in-house antibodies may not be widely used or not widely published. As more non-published user information is submitted, this database will continue improving and become more comprehensive.

Bioz

Bioz AI-based database listing data cards with supplier information (e.g., product number, supplier name, host species, clonality, purification process, isotype, concentration, storage, conjugation state, target protein, and references)

Advantages of Bioz

Bioz is free for academics, and allows users to search according to figures showcasing experiments where antibody has been used (e.g. WB blot, IHC, etc.). A cool feature it has is its own rating system based on times published, impact of publication, and how recent the antibody has been cited. Furthermore, it includes other reagents, not just antibodies.

Room for Improvement in Bioz

More limited in information than similar websites like BenchSci. However, as more users gain awareness, this should improve. Including RRID numbers would be helpful.

Antybuddy

Antybuddy is a reviewer site and database listing data cards with supplier information (e.g., product number, supplier name, clonality, application, supplier or user validation from publications, and user ratings with additional information on their user experience).

Advantages of Antibody Resource

Like Bioz, it has a rating system, but this time it is solely based on user information.

Room for Improvement in Antibody Resource

Antybuddy is a bit limited in information. However, as more users gain awareness, this should improve. The rating system is quality-based from the user experience, and not necessarily tied to data (e.g. figures of blots, etc, not often included). Including RRID numbers would also help standardize antibodies used.

pAbmAbs

pAbmAbs Reviewer site, which includes data cards with supplier information (e.g., company name, catalogue number, host species, target protein, clonality, and application)

Advantages of pAbmAbs

This site goes beyond a rating system based on users to include the protocols, protein target, and exact dilutions that the user used, and it runs competitions (monetary compensation) for user submitted data, which should encourage validation among users.

Disadvantages of pAbmAbs

Because it is fairly new, it’s data is somewhat limited. However, as more users gain awareness, this should improve. Another criticism, is that the user experience is not always tied to data (e.g. figures of blots, etc, not often included), nor does it include RRID numbers, which would be helpful

Main Limitation of Antibody Databases: Lacking the Protein Sequence

It is interesting to note that other than ABCD, antibody reagent databases do not include the sequence of the antibody itself. In industry, this is mainly for proprietary reasons. Yet confirming the amino acid sequence of the produced antibody would be an ideal way to ensure reproducibility. This is especially relevant for services such as CiteAb’s custom antibody generation for non-commercially available antibodies. With de novo antibody protein sequencing, creating a custom antibody would be easily facilitated and fast-tracked for scientists across industry and academia.

De novo antibody protein sequencing is also particularly significant for resources such as EuroMAbNet, the only database containing in-house generated antibodies. This type of database is incredibly useful for academic research as many antibodies used in research are not commercially available. As a result, many of these antibodies are generated in-house via immunization of animals to obtain:

1) polyclonal antibodies by affinity purifying animal serum, or

2) monoclonal antibodies through protein A/G purification from hybridoma supernatant.

Both of these methods suffer from batch-to-batch variability. However, reproducibility would be highly increased through mass spectrometry-based antibody protein sequencing for recombinant generation. Imagine what having the sequence would do to increase reproducibility, and to ensure project continuance in both academia and industry!

Storing the sequence of antibodies would also be valuable in case the product is discontinued, or the hybridoma cell line is lost. Referring to the RRID does not necessarily guarantee that the purchased antibody is identical to the one in the database/publication – variation between batches of antibodies produced is common. But using RRIDs in combination with recombinant antibodies generated through obtaining the protein sequence from antibody sequencing service would be a game changer.