Distributed and independent genome projects produce assemblies and annotations that can be beneficial to research on related species, if researchers can discover them. However, even a multi-species database that manages gene families may not contain all gene data of interest to the communities it serves. Services that assign new data, supplied by researchers or by other sites, to gene family memberships can help with discovery across databases by putting new sequence data into an evolutionary context, but then the data must be discoverable broadly.Applications that can operate where the data exists, to support comparative access for pre-publication and privately maintained genomes, can reduce the need to move large data sets among locations. For example, a group might generate a draft assembly of an accession with a novel phenotype that they have mapped to a certain genomic region. They may then wish to compare the scaffolds that contain the region of interest to a reference assembly for a different accession or for a related species, to find candidate genes that may be novel to their accession. Existing services such as CyVerse can be used to analyse data from many sources. Being able to do the comparison where the different genomes are located would save moving and duplicating large genome files, but requires considerable investment in distributed computation. Another solution is for GGB databases to host a local Galaxy instance connected to a Tripal database with public and private data sets. This is effective if a researcher with phenotypic,nft hydroponic genotypic and environmental data needs a place to house the data both before and after publication, but is not an expert in genomic analyses or data management.
Analysis pipelines tailored to the needs of a particular community, hosted through that community’s database, allow researchers to upload, search and visualize private data and public data, select these data and parameterize an association mapping workflow and execute that workflow locally. In order to execute the analysis remotely, data will need to move efficiently from the database to a remote analysis platform.Scientists often want to discover all that they can about a particular entity , but the data are distributed across multiple resources, many of which may be unfamiliar. Each data element on its own is not large, but the total space to be searched is. A hypothetical workflow is as follows: a researcher who works on one species comes to a participating database with a sequence of interest, wanting to find out what biological functions their sequence might be involved in. The researcher identifies homologous sequences in the new database by running BLAST. The database converts the BLAST results to an exchangeable token and queries other databases for information about orthologs. The product of these requests could be as simple as a gene name/symbol and a URL to point the user to the data display at the external database, or could also include provenance and database information for attribution, sequence, publications and many other types of information. For data discovery to work, databases with relevant data and compatible APIs must be discoverable and well documented, and a method should be in place to track usage across different services.There are several mechanisms for outreach to researchers. The most common form of outreach is meeting and conference attendance. With a large number of researchers at meeting and conferences GGB databases can use these opportunities for workshops, presentations or a database booth. GGB database brochures can be handed out during the meeting and conferences. However, there are a number of researchers that are unable to attend meeting and conferences so it is important that GGB database also use other forms of outreach. These include newsletters, mailing lists, blog posts and social media to inform researchers about new tools or data, webinars, workshops and videos.
These forms of outreach can be used together to reach a broader audience. Using social media during conferences and meetings with the appropriate hashtag can send information about new tools and data to researchers who cannot attend the conference. A prime example of this is the Plant and Animal Genome Conference, which has a strong social media presence.Many online resources and databases do not mention the people on their teams and only provide an anonymous contact form.Being anonymous creates a barrier to communication, and if contact/feedback forms don’t generate a response, there is no further recourse for the researcher to get help. Providing individual staff contact information and even photographs makes it easier for researchers to target questions to the appropriate person. Photos can enable researchers to find curators at meetings, and in general encourage communication by putting, literally, a human face on the GGB resources. Building in dedicated time at workshops for a ‘meet the team’ event, well advertized in advance to the research community, is also recommended to increase engagement opportunities.Overcoming the challenge of reliable data submission will require communication among representatives from the appropriate journals, GGB databases and funding agencies to establish guidelines and an easy-to-submit and police system for researchers and the journals/funding agencies and databases. This would likely be best initiated through an inter-agency sponsored workshop, followed up by regular meetings and assessment of effectiveness. Such a workshop could also develop ways to ensure journal publishers and editors are aware of all relevant GGB databases so they can direct authors of each accepted paper to the proper repository, nomenclature clearing house etc.
Providing access to centralized cyber infrastructure where databases, journals and funding agencies could sign off on successful data submission for projects would help make this process easier for all parties and ensure accountability.The GGB databases that currently comprise the AgBioData Consortium were created to serve the needs of researchers for access to curated and integrated data and analysis/visualization tools to aid scientific discovery, translation and application. The funding for these databases, however, is limited and not stable. Maintaining these resources in the longer term so that invaluable data are kept up-to-date and do not get lost is a major issue facing almost all AgBioData databases, their researcher communities and funding agencies.AgBioData databases are supported through a variety of sources. Generally these fall into one of four categories: primarily supported through line-item government funding, such as the USDA-ARS databases MaizeGDB, SoyBase, GrainGenes, Legume Information System and GRIN; primarily supported through competitive federal grants, such as TreeGenes, Hardwood Genomics, Gramene, Planteome, Solanaceae Genomics Network and Araport; supported through a combination of competitive federal grants, commissions and industry, such as the Genome Database for Rosaceae, AgBase, PeanutBase, AnimalQTLdb and CottonGen; and supported primarily through a user subscription model, such as TAIR. With long-term government funding, the USDA-ARS databases enjoy the most stable financial support of the AgBioData databases. They typically represent high-value commodity crops serving a large research and industry community. While the level of support provided by USDAARS generally allows for continuation of base activities and curation, it typically does not provide resources for technical innovation or more resource-efficient systems to be implemented. For these, funding through competitive grants is increasingly necessary,nft system as in the case of the NSF funded Legume Federation award. At the other extreme lies TAIR, which after a phased withdrawal of support by NSF, successfully implemented a subscription-type funding model under a not-for-profit organizational structure.
As the model plant for functional genomics, TAIR also has a large user community making this funding option more feasible to implement than for the databases represented in categories 2 and 3. Many of the AgBioData databases have reported willingness of the scientific stakeholders to budget some funds in their grants to support data deposit and access to their community databases, similar in how they budget for peer reviewed, open access publications costs. Unfortunately, most of the databases do not have organizational structures or processes that would allow them to accept these funds.How can studies of agricultural systems and the ways that people interact with foods they produce, eat, and discard lead us to new understandings about social relations in the past? How do labor roles, gender relations, and status-based inequalities relate to these types of interactions? This dissertation addresses these themes through the lens of food ways in the prehispanic Moche Valley of north coastal Peru. The Peruvian north coast witnessed a profound series of social and political changes during a time period that archaeologists refer to as the Early Intermediate Period, or EIP , with far-flung consequences for members of various social standing, from rural households to political centers. The EIP was marked by an increase in political complexity, with clear shifts in settlement and site reorganization accompanied by an increase in social stratification . These cultural and political changes occurred in a vertically compressed environment that also witnessed periodic El Niño events, which had significant and varied impacts on people’s subsistence practices. Indeed, substantial changes in elevation over the relatively short distance from the coast to the highlands, in the Moche and neighboring river valleys, create different micro-environments within close proximity to one another. Fertile interande an valleys have constituted a prime interaction zone between people of the highlands and the densely populated Peruvian coast, a contact dynamic that initiated in prehistory and continues today.The beginning of the EIP, which includes the Salinar and Gallinazo phases, witnessed the abandonment of earlier ceremonial centers; population increases and expansion of irrigation systems; political fragmentation and the appearance of formal fortifications and settlements in defensive locations; and cooperation and conflict between coastal and highland groups and among polities of various coastal valleys . Between approximately 300 and 800 A.D., the iconic Moche culture flourished on the Peruvian north coast.
The large adobe pyramid complex of the Huacas de Moche was constructed, accompanied by the emergence of a new regional political economy in which Moche rulers exercised significant economic, military, and ideological power over the population of the Moche and adjacent valleys. How did these periods of profound social change affect the prehispanic residents of the Moche Valley in terms of gender relations, status, and the organization of labor in ancient rural households? Foodways data provide a critical lens for examining these issues. Foodways represent a fundamental axis along which identity is constructed and maintained, and are increasingly recognized as having played a prominent role in the emergence of social hierarchies and the negotiation of status and power . In this dissertation, I incorporate archaeobotanical, environmental, and ethnohistorical evidence to address changes in food production, processing, and consumption during the EIP, a period that included the consolidation of the Southern Moche polity, one of the largest and most complex pre-Columbian political systems in the New World. Conducted inconjunction with MOCHE, Inc., a 501c3 nonprofit dedicated to protecting archaeological sites through community heritage empowerment, this project involved a large-scale comparative analysis of paleoethnobotanical data sampled from five EIP habitation sites that span the period of political transformation and state formation in the Moche Valley. The data presented in this dissertation derive from three major projects conducted in the Moche Valley in collaboration between North American and Peruvian archaeologists since 2000: the Moche Origins Project , directed by Brian Billman and Jesus Briceño Rosario ; el Proyecto de Evaluación Arqueológico con Excavaciones en las Lomas de Huanchaco , directed by Gabriel Prieto and Victor Campaña ; and the Galindo Archaeological Project , directed by Gregory Lockard and Francisco Luis Valle . I employ diachronic and spatial analyses of archaeobotanical data from 225 soil samples recovered from five domestic habitation sites excavated within the contexts of these projects to address key issues that have largely remained untested with direct subsistence data. Through these analyses, I trace changes in food production and wild plant food collection during the EIP, considering issues of agricultural intensification and the resulting impacts on labor relations, gender roles, and social inequality for the pre-Columbian inhabitants of rural households in the Moche Valley. The question of scale looms large in this dissertation. The Moche civilization of northern Peru is one of the best-known and most intensely studied archaeological cultures of the ancient New World. The ancient Moche have captured the imagination of scholars and the public alike, characterized by a series of elaborately decorated temple complexes, wealthy elite burials, and exquisite ceramics found over ten river valleys on the desert coast.