Update Nav menu and add Intro blurb

[yuanzhou]

Based on @emquardokus's feedback from https://github.com/hubmapconsortium/antibody-api/issues/166#issuecomment-2083037998

It would also be great to have an introduction to what the AVR website is for which many have asked or have misinterpreted based on interactions at several meetings or in discussions with TMCs. Another important change would be the ADD AVRs since this is limited not to everyone and should continue to be so reviews can occur prior to adding AVRs. Some suggestions we had:

• "Add AVRs" hyperlink currently directs to Globus. May want to change to avoid people trying to submit through Globus!
• Could link something like "Learn more about AVRs at ARWG" and hyperlink to https://hubmapconsortium.org/open-working-groups/
• Could link "AVR SOP" with hyperlink https://zenodo.org/doi/10.5281/zenodo.7418623, which will not change even as we publish new versions of SOP

Update the nav items and add intro blurb as shown in the below mockup:

[yuanzhou]

@emquardokus we are including your request to the upcoming sprint, can you send an introduction paragraph about AVR? Can you also take a look at the mockup and see if everything gets reflected?

[emquardokus]

@yuanzhou we would like to use this paragraph to introduce AVRs on the AVR website; it comes from our SOP. Antibody validation reports (AVRs) provide information on the characterization of individual antibodies for multiplexed antibody-based imaging assays. AVRs additionally report details not included by antibody vendors such as the best performing conjugate for a particular clone and/or the impact of cycle order on immunogenicity. The current AVR database, on the Human Biomolecular Atlas Program (HuBMAP) AVR Search website, allows validated antibodies to be queried by clone, Research Resource Identifiers (RRIDs), catalog number, organ/tissue, and HuBMAP platform. This AVR metadata is included in a .CSV file uploaded to the portal by the contributing author for all AVRs submitted at one time. The AVR is completed as a text file and saved as a PDF for submission to the HuBMAP AVR upload site; it contains additional characterization data. Results from queries of the database may be downloaded as a .CSV and individual AVRs may be downloaded and viewed as a PDF.

AVRs were piloted to provide individual antibody validation information for the diverse antibody-based methods employed by HuBMAP members. Importantly, AVRs have become tightly integrated with Organ Mapping Antibody Panels (OMAPs) (https://humanatlas.io/omap), a comprehensive panel of curated antibodies that identifies the major anatomical structures and cell types present in a specific organ. The selected antibodies are optimized for a tissue preservation method and multiplexed imaging modality. Both efforts share standardized metadata fields that will facilitate construction of a searchable antibody database. Beginning in 2023, we are excited to open AVR contributions to the larger community, beyond HuBMAP members.

[yuanzhou]

@emquardokus two things to confirm:

• Do you still want to keep "AVR SOP" link in the top menu? As shown in the mockup.
• How do you prefer to handle the "Add AVRs" or just remove it?

[emquardokus]

@yuanzhou @shirey 1) AVR SOP and AVR FAQ should both be linked from top menu 2) Need to have meeting to discuss---Add AVRs has a complicated history--we don't want the button as prominent and confusing to researchers as the process was changed 100% for how this works compared to v1.0 version of Website---this might be better to schedule a meeting to walk through since the way we really want this to go ultimately is to submit for review rather than submit to immediately go live by original authors. The Affnity reagents working group (ARWG) folks would review the AVRs, comment, revisions would be made and the final versions would be uploaded by us to go live. It used to immediately go live to AVR website and quality was poor at best with no standardization until ARWG set up a process. Right now we collect everything via google sheets, review, author revise, we finalize and upload. 3) Noticed a problem in the header paragraph due to the change in process that needs to be corrected, but is dependent on conversation in 2) above. This section of paragraph needs to be fixed as it does not reflect the new process. "This AVR metadata is included in a .CSV file uploaded to the portal by the contributing author for all AVRs submitted at one time. The AVR is completed as a text file and saved as a PDF for submission to the HuBMAP AVR upload site; it contains additional characterization data. "