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Looking for a database of plant features

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To perform some private data science experiments I am looking for accessible information on morphological plant features (tabular information would be best). Crawling the web I found many websites with limited more general description and a lot of information on location and population data.

Do you know a website, institute or person in possession of such data and willing to share it? Since I am located in Germany my main interest is in the local flora, but any other would also do the job.


-- Traits --

TRY

TRY is a Plant Trait Database. More formally, it's a network of vegetation scientists headed by DIVERSITAS/IGBP, and the Max Planck Institute for Biogeochemistry, providing a global archive of curated plant traits.

BioTraits

This is an online resource for empirical data on how biological traits respond to environmental drivers such as temperature, light, and salinity.

Nate Swenson

Nate and his collaborators have compiled a ton of traits for species all over the world (though focused on the tropics).

Coyle et al. 2014

Appendix 2 of their 2014 Ecography paper lists primary literature sources and publicly available trait databases they used to examine 3 traits: leaf nitrogen, seed mass, and wood density.

-- Images --

Morphbank

An international Web database that contains thousands of high-resolution photographs and other images of plant and animal specimens.

Botanical Images Databases

This site provides dozens of links to databases containing plant images. There are also regional databases provided (e.g., Pflanzenphotos.de).

Botany.ch

This site contains both text sources (e.g., lectures and essays) as well as links to morphology picture databases (e.g., Botanical Image Database of the University of Basel).


See also FAO Online Catalogues for a number of morphological sources in both English and German.


There is the TRY database of plant traits:

https://www.try-db.org/TryWeb/Home.php


Database of vegetation of planet Earth

It's a treasure trove of data: the global geodatabase of vegetation plots "sPlotOpen" is now freely accessible. It contains data on vegetation from 114 countries and from all climate zones on Earth. The database was compiled by an international team of researchers led by Martin Luther University Halle-Wittenberg (MLU), the German Centre for Integrative Biodiversity Research (iDiv) and the French National Centre for Scientific Research (CNRS). Researchers around the world finally have a balanced, representative dataset of the Earth's vegetation at their disposal, as the team reports in the journal Global Ecology & Biogeography.

Global issues and questions require global answers. "If we want to understand or predict how climate change will affect biodiversity in all regions on Earth, we have to consider them in their entirety. We need more than just data from a few well-studied regions," explains Professor Helge Bruelheide, a geobotanist at MLU and a member of iDiv. Instead, a global geodatabase is required with information on vegetation from all continents and climate zones.

Now, with the launch of "sPlotOpen," this database not only exists but it can be accessed by anyone who is interested. Around 100,000 vegetation plots from 114 countries have been entered into the database which has been release as open access. Each data point contains information on all of the plant species co-occurring at that location, alongside geographical, temporal and methodological metadata. This enables researchers to see exactly when, where and by whom the data point was collected.

Most importantly, sPlotOpen provides information about the complete plant community that can be found at the respective location. This is one of the great advantages of the new database, explains Dr Francesco Maria Sabatini from MLU and iDiv, who is coordinating the project together with Dr Jonathan Lenoir from the CNRS. "There are already several databases that show the distribution of individual plant species worldwide. In reality, however, plant species rarely occur alone and in isolation," says the researcher. With the aid of "sPlotOpen," scientists could figure out whether the data was collected from a forest -- with various tree and grass species -- or a meadow. According to the biologist, this is important when selecting individual surveys for specific research projects that are meant to investigate, for instance, only forests or grasslands.

Another advantage is that the team has attempted to balance the data. "There is already an incredible wealth of data on vegetation in Europe, North America and Australia. But, for many different reasons, there is much less data on other regions," says Sabatini. If the data from all countries were compared without weighting it first, false conclusions could be drawn. Therefore, the team tried to establish a certain comparability between the datasets from different regions. For example, not all data from Western Europe was included in the project -- only a representative selection. The team already balanced the data for the benefit of future users. This should prevent a striking imbalance of data over regions that are less well documented, for example, warm or cold, dry or humid climates. "Our database has the potential to be a gamechanger for research projects in the field of macroecology and beyond," explains Sabatini. It could also be used in the field of geoscience, for example, to train algorithms for analysing satellite images. If you know where a certain community of plants exists, you can associate this plant community to a specific pattern in satellite images, namely a specific spectral community, and search other images for the same patterns.

In order to create this unique set of data, the team from Germany and France have relied on the support of 161 researchers from 57 countries who participated in the project by providing data. "Behind these individual datasets are countless colleagues and students, who went to the field collecting data in the first place. The sPlotOpen database could not exist without them" says Sabatini. The data also comes from national projects, such as the German Vegetation Reference Database, which is managed at MLU by Helge Bruelheide's research group.


Seeds and their Morphological Features (With Diagram)

Gram seed (Fig. 8.2) is a dicot, non-endospermic seed. The seeds are produced within the pods or leguminous fruits.

A gram seed appears conical-pyriform in outline.

It has following parts:

It consists of two layers-outer testa and inner tegmen. Testa is thick and brownish. The tegmen is thin, membranous, and whitish and remains fused with testa. The pointed beak like end of the seed has a minute pore called micropyle. If a soaked seed is gently pressed, a drop of water oozes out of the micropyle. A small oval scar seen near the micropyle is called hilum through which the seed was attached to fruit. Another oval scar present in the middle is called chalaza or strophiole. A distinct ridge called raphe runs from hilum to chalaza.

It presents inner to seed coat. It consists of two circular yellowish cotyledons that are attached to the embryo axis. The part of embryo axis above the point of attachment to the cotyledons is called epicotyle. The tip of epicotyle is called plumule. Similarly, the region of the embryo axis below the point of attachment of cotyledons is called the hypocotyle. The tip of hypocotyle is called radicle. During germination, the radicle comes out first through the micropyle and grows to form a tap root. The plumule gives rise to shoot system.

2. Morphology of Castor Seed (Ricinus communis):

Castor seed is a monocot, endospermic seed. The castor seeds are produced within a schizocarpic fruit called the regma which on maturity breaks up into 3 cocci, each containing a single seed. A castor seed is roughly oblong in outline with distinct convex (dorsal) and flat (ventral) surfaces. A castor seed has following parts (Fig. 8.3)

It is the outer layer of seed coat. It is thick, hard and brittle. The external surface appears smooth, shinning and mottled brown in colour.

It is the inner layer of seed coat that appears dull and papery. Now it is called as perisperm or persistent nucellus.

It is a white spongy bilobed outgrowth present near the narrow end of the seed. If partially covers the hilum (dark scar) and completely covers the micropyle (small pore). Caruncle absorbs water which percolates through the micropyle into the seed.

It is a shallow ridge present on the testa of flat surface of the seed. The distinct bifurcation of raphae represents chalaza.

It is a white oily food storage tissue that is present inner to the perisperm. From this layer castor oil of commerce is extracted.

Embryo lies in the centre of endosperm. It consists of a radicle, a plumule and two lateral cotyledons, all of which are present on a short embryo axis. The cotyledons are thin, semi-transparent and oval in outline. They have palmate venation. The middle costa or rib is more prominent and bears a few lateral veins.

Radicle lies outside the cotyledons towards the micropylar end. It is a knob-like outgrowth. Plumule lies in between the two cotyledons and is quite indistinct. Epicotyl is also indistinct. In between the place of origin of the two cotyledons and the radicle is present a short hypocotyl. Castor-oil seed is dicotyledonous (having two cotyledons), endospermic (with a special food storing tissue called endosperm) and perispermic (having perisperm or persistent nucellus).

3. Morphology of a maize seed (Zea mays):

Maize or Corn seed (Fig. 8.4) is actually a one seeded fruit called caryopsis or grain. It is a monocot endospermic seed.

It consists of following parts:

It is fused with the fruit wall (pericarp). It encloses a kernal which includes embryo and endosperm.

It constitutes 2/3 of the grain. Endosperm consists of outer aleurone layer and inner starchy endosperm.

It lies on one side of the starchy endosperm and appears to be a lighter oval area in the whole seed. Embryo consists of a scutellum and a short embryo axis (tigellum). The scutellum is a shield-shaped cotyledon attached to a node of embryo axis. The surface of scutellum facing endosperm is called epithelial layer. It is both secretory and absorptive in nature. The epithelial layer secretes hormones into the endosperm for the synthesis of enzymes required for solubilisation of food. The solubilised food is absorbed by it and then transferred to the embryo axis.

The embryo axis has plumule (upper end) and radicle (lower end). The plumule contains a few rudimentary leaves and a conical protective sheath called coleoptile. The coleoptile has a termina pore for the emergence of first leaf during germination. The sheath is capable of growth. It assists the future shoot in passing through the soil during germination.

The radicle has two protective sheaths, inner root cap and outer coleorhiza. Roughly in the middle of embryo axis arises a vascular strand. It ramifies into the scutellum. The place of origin of the vascular strand from the embryo axis is called cotyledonary node.

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The Garden.org Plants Database

Found one starter plant of this marked down to a buck at the grocery store. This is late for me to plant peppers, but I decided if it grew one pepper, it was a payoff. Will try to report later. I think it may be marketed more for commercial growers.

A beautiful and fragrant white trumpet from China that has a yellowish-greenish throat and varying amounts of green and pink-purple to brown color on the reverse of the petals. This species has played a major role in producing today's trumpet hybrids. Vigorous and long lived it will do great in any garden if drainage is perfect. Covering against excessive winter rain is a must. It will produce big bulbs over time. Easy to grow from seeds.

I thought this was the most beautiful flower I had ever seen when I first saw the picture, so I ordered it. What a disappointment! It wasn't at all like the color in the picture. Instead of the creamy white you see in the picture, it's a light apricot color and the deep purple isn't very purple at all, it's more of a magenta/maroon color. I thought maybe it would look more like the picture the second year, but no, it's the same unremarkable colors I described. I've seen far prettier daylilies than this and have several I like better. But I have found that mose daylily sellers don't pay much attention to color correction when they post pictures of their daylilies. In this day and age of photoshop and color consistent monitors, it's disingenuous to post incorrect colors to their ads. And I have never had one of the blossoms on this variety that had any of the doubling shown in this picture. It's pretty, but nothing special and I wouldn't ever have spent that kind of money had I known the true colors of this overpriced plant


Angiosperms (With Diagram) | Plant Kingdom

Angiosperms are those seed plants in which seeds are formed inside fruits and the sporophylls are organised into flowers.

1. Flowering plants or angiosperms are the most recently and highly evolved plants. They appeared on earth about 130 million years ago. First angiosperm fossil recorded from mid cretaceous period is Archaefructus from China and Archaeanthus from Canada.

2. They are the most abundant and conspicuous plants with about 270,000 (220,000 dicots and 50,000 monocots) species.

3. Flowering plants occur in most environments on the earth. Sea is the only exception. Here only two angiosperms are found. They are Zostera and Thalassia. Wolffia is smallest (0.1 cm) while Eucalyptus regnans is largest (114 m height). Angiosperms are most wide­spread in plains as well as hills.

They have been recorded at an altitude of 6000 m in the Himalayas or permanently frozen Antarctica. Even deserts possess flowering plants. Some of these desert plants are able to grow soon after good shower, flower and shed seeds in a few weeks of wetness available in the area. One species is reported to occur in hot springs at 60°C.

A small orchid lives underground. It has mycorrhizal association which helps it obtain nourishment from decaying organic matter. In moist areas some plants grow perched on other plants. They are dependent upon the larger plant for space only (neither food nor water). Such plants are called epiphytes. Epiphytes are popularly known as space hosts, e.g., Vanda.

4. Sporophylls are aggregated to form flowers. Therefore, angiosperms are also called flowering plants.

5. Both microsporophyIIs and megasporophylls are specialised. A microsporophyll or stamen consists of a filament and an anther. A megasporophyll or carpel is rolled and partly sterilized to produce a stigma, style and ovary containing ovules. Within ovules are present highly reduced female gametophytes known as embryo sacs. Embryo sac formation is preceded by meiosis. So all the cells of embryo sac are haploid.

6. Pollination is through several agencies but most prominent amongst them is by ani­mals, especially insects. The flowers possess showy petals, edible pollen or nectar for this.

7. Pollen grains or microspores reach stigmatic surface found at the tip of carpel or megasporophyll.

8. Female gametophyte or embryo sac develops up to 8-nucleate state prior to fertilisation. There is a three cell egg apparatus (one egg cell or oosphere and two synergids), three antipodal cells and two polar nuclei. The two polar nuclei fuse to form a diploid secondary nucleus.

9. Archegonia are absent. Instead, there is one oosphere surrounded by two specialised synergid cells that attract the pollen tube. The latter brings two naked non-flagellate male gametes.

10. There is double fertilisation. One male gamete fuses with oosphere or egg cell to form zygote. It is called generative fertilization or syngamy. The second male gamete fuses with diploid secondary nucleus to form triploid primary endosperm nucleus (PEN). It rep­resents vegetative fertilization. The latter is also called triple fusion since three nuclei are involved in its formation. Total 5 nuclei take part in double fertilization.

11. Zygote develops into embryo. Central cell containing triploid primary endosperm forms triploid endosperm. Endosperm provides nourishment to developing embryo. Syner­gids and antipodals degenerate after fertilization.

12. Fertilized ovules ripen into seeds. The seeds are covered by fruits. A fruit is technically a ripened ovary. Fruits not only protect the seeds but also help in their dispersal.

13. Xylem contains ves­sels.

14. Phloem possesses sieve tubes and companion cells.

15. Secondary growth occurs in stem and root of some angiosperms, placed in group dicots.

Flower is basically a shoot which has been modified in angiosperms for carrying out the process of sexual reproduction. A flower has a limited growth with a long inter-mode at the base (appearing as stalk or pedicel) and condensed nodes present on thalamus or torus. The latter bears four types of structures— sepals, petals, stamens and carpels.

Sepals and petals are sterile floral leaves. Sepals are green and cover the flower in the bud condition. They are protective in nature. Petals are showy and are meant for attracting animal polli­nators, especially insects. Stamens are specialized microsporophyll’s. Each stamen has a narrow stalk or filament and a knob-like broader tip celled anther.

Anther develops four microsporangia or pollen sacs. The latter produce microspores or pollen grains. Carpels are specialized megasporophylls. They may be free or fused. Each carpel has a swollen base named ovary.

The interior of ovary contains one or more placentae (singular- placenta) for bearing ovules. The tip of the carpel has sticky tip known as stigma. Stigma is meant for receiving pollen grains. Stigma is connected with ovary through a stalk known as style.

The transfer of pollen grains or microspores to the receptive area of megasporophyll or stigma is called pollination. Cross pollination is common in which pollen grains of one flower reach the stigma of another flower. In gymnosperms, cross pollination is accom­plished by wind.

The same is known as anemophily. In angiosperms wind pollination or anemophily takes place in a few cases. In most of the plants, pollination is effected by animal’s insects, worms, birds, bats and even human beings. Insects out-number all other animals as pollinators.

After falling on the stigmas, the pollen grains germinate and develop pollen tubes. The latter descend the styles enter the ovary and then ovules to perform fertilization. After fertilization the ovules mature into seeds. The ovary containing the seeds ripens into a fruit. The name angiosperm for flowering plants is derived from their characteristics of having covered seeds or seeds enclosed inside the fruits.

The fruit not only protects the seeds during their ripening but also aids in seed dispersal. Some dry fruits have explosive mechanism to throw the seeds. Other dry fruits have devices to stick to the fur of animals or float in air and water. There are other fruits in which the fruit wall is fleshy.

The fleshy ripe fruits attract and tempt animals, especially birds, to eat them. However, seeds of fleshy fruits remain unharmed by their picking or even after passing through their digestive tracts. The animals disperse the seeds during the process of feeding on fruits.

Flowering plants have thus exploited insects, birds and several other animals as agents of pollination, fruits and seed dispersal. It is one major reason for present day dominance of flowering plants.


Watershield (Brasenia schreberi)

Watershield is an aquatic, perennial herb with floating leaves that grows in ponds, lakes, and slow moving streams. It is widespread in North America, and is found in South and Central America, the West Indies, eastern Asia, Africa, and eastern Australia. It is a member of the Cabombaceae (watershield) family.

Watershield is easily recognized by its leaves. They are oval shaped, peltate (the leaf stem attaches to the leaf in the middle of the blade, like a mushroom stalk), with the undersides covered with thick, jelly-like slime. Leaf blades are small, ¾ to 2½ inches wide and 1 to 4½ inches long. The top of the leaves are green, while the undersides and leaf stems are reddish purple. All underwater parts of this plant are covered with slime. This thick coat apparently protects plants from drying out during drought and may also deter mammals from eating it.

The flowers of watershield are small and inconspicuous, typical of wind-pollinated plants. Flowers have three to four sepals about ¾ inches long that are green underneath and reddish purple to maroon on top. There are usually four petals that are slightly longer and thinner than the sepals. They are reddish purple to maroon in color. Flowers usually have 18-36 stamens and 4-18 pistils in each flower.

Although watershield flowers are not showy, they have an interesting biology. Flower buds develop underwater and are covered with slime. Flowers bloom over a two-day period. On the first day the bud emerges above the water. Sepals and petals open and bend downward. Although stamens and pistils are present in each flower, on the first day of blooming, only the pistils emerge. Stalks of the pistils lengthen and spread outward over the petals. At night, the flower stalk bends and the flowers submerge beneath the water. On the second day, flowers emerge from the water again, but with the pistils retracted. The stamen stalks are lengthened and the anthers open. In this way flowers are cross-pollinated (Osborn and Schneider). After blooming, the sepals and petals fold up and submerge. Fruit develops underwater enclosed in the petals and sepals. Fruits are leathery and club shaped with one or two seeds each.

Although watershield is native to North America, it can become extremely weedy. This plant can quickly take over shallow ponds and lakes. It sometimes becomes so dense that it slows boat travel. Watershield plants secrete a number of chemicals that kill or inhibit growth of a wide range of bacteria, algae, and other plants (Elakovich and Wooten). By this mechanism, watershield kills off competing vegetation.

Although watershield can be a nuisance, it does benefit wildlife and has been used by humans. Waterfowl eat this plant. Its floating leaves provide shelter for fish and other aquatic organisms. Native Americans reportedly ate its tuberous roots. Young leaves and stems not yet covered in slime are eaten as salad greens in parts of Japan.

For More Information

References

Elakovich, Stella D., and Jean W. Wooten. 1987. Journal of Chemical Ecology. An examination of the phytotoxicity of the watershield, Brasenia schreberi. Vol. 13 (9): 1935-1940.

Flora of North America Editorial Committee, editors (FNA). 1997. Volume 3, Magnoliophyta: Magnoliidae and Hamameliidae. Oxford University Press, New York, NY. Accessed through: Flora of North America Online.

Godfrey, Robert K., and J. W. Wooten. 1981. Aquatic and wetland plant of the southeastern United States, dicotyledons. University of Georgia Press, Athens, Georgia.

Osborne, Jeffrey M., and Edward L. Schneider. 1988. Morphological studies of the Nymphaeaceae Sensu Lato. XVI. The floral biology of Brasenia Schreberi. Annals of the Missouri Botanical Garden. Vol. 75 (3): 778-794.

Yatskievych, George. 2006. Steyermark’s Flora of Missouri Volume 2, Revised Edition. Missouri Botanical Garden Press, St. Louis. Missouri.


Nomenclatural coverage

The Plant List aims to provide all the scientific names for species for these plant groups. A breakdown of the numbers of plants and names included in each plant group is provided, see Statistics. Coverage of infraspecific taxa (subspecies, varieties, forms etc) is not comprehensive they are included, primarily where they are synonyms or accepted names for species names.

Coverage and data quality are primarily influenced by the source data sets used to build The Plant List . We are aware of additional data sets which, had they been included, would have enriched and improved the final product. We hope to include such data sets in later releases.


Looking for a database of plant features - Biology

A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.

A curated set of metadata for culture collections, museums, herbaria and other natural history collections. The records display collection codes, information about the collections' home institutions, and links to relevant data at NCBI.

A collection of genomics, functional genomics, and genetics studies and links to their resulting datasets. This resource describes project scope, material, and objectives and provides a mechanism to retrieve datasets that are often difficult to find due to inconsistent annotation, multiple independent submissions, and the varied nature of diverse data types which are often stored in different databases.

The BioSample database contains descriptions of biological source materials used in experimental assays.

Database that groups biomedical literature, small molecules, and sequence data in terms of biological relationships.

A collection of biomedical books that can be searched directly or from linked data in other NCBI databases. The collection includes biomedical textbooks, other scientific titles, genetic resources such as GeneReviews, and NCBI help manuals.

A resource to provide a public, tracked record of reported relationships between human variation and observed health status with supporting evidence. Related information in the NIH Genetic Testing Registry (GTR), MedGen, Gene, OMIM, PubMed and other sources is accessible through hyperlinks on the records.

A registry and results database of publicly- and privately-supported clinical studies of human participants conducted around the world.

A centralized page providing access and links to resources developed by the Structure Group of the NCBI Computational Biology Branch (CBB). These resources cover databases and tools to help in the study of macromolecular structures, conserved domains and protein classification, small molecules and their biological activity, and biological pathways and systems.

A collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality.

A collection of sequence alignments and profiles representing protein domains conserved in molecular evolution. It also includes alignments of the domains to known 3-dimensional protein structures in the MMDB database.

The dbVar database has been developed to archive information associated with large scale genomic variation, including large insertions, deletions, translocations and inversions. In addition to archiving variation discovery, dbVar also stores associations of defined variants with phenotype information.

An archive and distribution center for the description and results of studies which investigate the interaction of genotype and phenotype. These studies include genome-wide association (GWAS), medical resequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits.

Includes single nucleotide variations, microsatellites, and small-scale insertions and deletions. dbSNP contains population-specific frequency and genotype data, experimental conditions, molecular context, and mapping information for both neutral variations and clinical mutations.

The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis. GenBank consists of several divisions, most of which can be accessed through the Nucleotide database. The exceptions are the EST and GSS divisions, which are accessed through the Nucleotide EST and Nucleotide GSS databases, respectively.

A searchable database of genes, focusing on genomes that have been completely sequenced and that have an active research community to contribute gene-specific data. Information includes nomenclature, chromosomal localization, gene products and their attributes (e.g., protein interactions), associated markers, phenotypes, interactions, and links to citations, sequences, variation details, maps, expression reports, homologs, protein domain content, and external databases.

A public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted and tools are provided to help users query and download experiments and curated gene expression profiles.

Stores curated gene expression and molecular abundance DataSets assembled from the Gene Expression Omnibus (GEO) repository. DataSet records contain additional resources, including cluster tools and differential expression queries.

Stores individual gene expression and molecular abundance Profiles assembled from the Gene Expression Omnibus (GEO) repository. Search for specific profiles of interest based on gene annotation or pre-computed profile characteristics.

A collection of expert-authored, peer-reviewed disease descriptions on the NCBI Bookshelf that apply genetic testing to the diagnosis, management, and genetic counseling of patients and families with specific inherited conditions.

Summaries of information for selected genetic disorders with discussions of the underlying mutation(s) and clinical features, as well as links to related databases and organizations.

A voluntary registry of genetic tests and laboratories, with detailed information about the tests such as what is measured and analytic and clinical validity. GTR also is a nexus for information about genetic conditions and provides context-specific links to a variety of resources, including practice guidelines, published literature, and genetic data/information. The initial scope of GTR includes single gene tests for Mendelian disorders, as well as arrays, panels and pharmacogenetic tests.

Contains sequence and map data from the whole genomes of over 1000 organisms. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life (bacteria, archaea, and eukaryota) are represented, as well as many viruses, phages, viroids, plasmids, and organelles.

The Genome Reference Consortium (GRC) maintains responsibility for the human and mouse reference genomes. Members consist of The Genome Center at Washington University, the Wellcome Trust Sanger Institute, the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information (NCBI). The GRC works to correct misrepresented loci and to close remaining assembly gaps. In addition, the GRC seeks to provide alternate assemblies for complex or structurally variant genomic loci. At the GRC website (http://www.genomereference.org), the public can view genomic regions currently under review, report genome-related problems and contact the GRC.

A centralized page providing access and links to glycoinformatics and glycobiology related resources.

A database of known interactions of HIV-1 proteins with proteins from human hosts. It provides annotated bibliographies of published reports of protein interactions, with links to the corresponding PubMed records and sequence data.

A collection of consolidated records describing proteins identified in annotated coding regions in GenBank and RefSeq, as well as SwissProt and PDB protein sequences. This resource allows investigators to obtain more targeted search results and quickly identify a protein of interest.

A compilation of data from the NIAID Influenza Genome Sequencing Project and GenBank. It provides tools for flu sequence analysis, annotation and submission to GenBank. This resource also has links to other flu sequence resources, and publications and general information about flu viruses.

Subset of the NLM Catalog database providing information on journals that are referenced in NCBI database records, including PubMed abstracts. This subset can be searched using the journal title, MEDLINE or ISO abbreviation, ISSN, or the NLM Catalog ID.

MeSH (Medical Subject Headings) is the U.S. National Library of Medicine's controlled vocabulary for indexing articles for MEDLINE/PubMed. MeSH terminology provides a consistent way to retrieve information that may use different terminology for the same concepts.

A portal to information about medical genetics. MedGen includes term lists from multiple sources and organizes them into concept groupings and hierarchies. Links are also provided to information related to those concepts in the NIH Genetic Testing Registry (GTR), ClinVar, Gene, OMIM, PubMed, and other sources.

A comprehensive manual on the NCBI C++ toolkit, including its design and development framework, a C++ library reference, software examples and demos, FAQs and release notes. The manual is searchable online and can be downloaded as a series of PDF documents.

Provides links to tutorials and training materials, including PowerPoint slides and print handouts.

Part of the NCBI Handbook, this glossary contains descriptions of NCBI tools and acronyms, bioinformatics terms and data representation formats.

An extensive collection of articles about NCBI databases and software. Designed for a novice user, each article presents a general overview of the resource and its design, along with tips for searching and using available analysis tools. All articles can be searched online and downloaded in PDF format the handbook can be accessed through the NCBI Bookshelf.

Accessed through the NCBI Bookshelf, the Help Manual contains documentation for many NCBI resources, including PubMed, PubMed Central, the Entrez system, Gene, SNP and LinkOut. All chapters can be downloaded in PDF format.

A project involving the collection and analysis of bacterial pathogen genomic sequences originating from food, environmental and patient isolates. Currently, an automated pipeline clusters and identifies sequences supplied primarily by public health laboratories to assist in the investigation of foodborne disease outbreaks and discover potential sources of food contamination.

Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings.

A collection of nucleotide sequences from several sources, including GenBank, RefSeq, the Third Party Annotation (TPA) database, and PDB. Searching the Nucleotide Database will yield available results from each of its component databases.

A database of human genes and genetic disorders. NCBI maintains current content and continues to support its searching and integration with other NCBI databases. However, OMIM now has a new home at omim.org, and users are directed to this site for full record displays.

Database of related DNA sequences that originate from comparative studies: phylogenetic, population, environmental and, to a lesser degree, mutational. Each record in the database is a set of DNA sequences. For example, a population set provides information on genetic variation within an organism, while a phylogenetic set may contain sequences, and their alignment, of a single gene obtained from several related organisms.

A collection of related protein sequences (clusters), consisting of Reference Sequence proteins encoded by complete prokaryotic and organelle plasmids and genomes. The database provides easy access to annotation information, publications, domains, structures, external links, and analysis tools.

A database that includes protein sequence records from a variety of sources, including GenPept, RefSeq, Swiss-Prot, PIR, PRF, and PDB.

A database that includes a collection of models representing homologous proteins with a common function. It includes conserved domain architecture, hidden Markov models and BlastRules. A subset of these models are used by the Prokaryotic Genome Annotation Pipeline (PGAP) to assign names and other attributes to predicted proteins.

Consists of deposited bioactivity data and descriptions of bioactivity assays used to screen the chemical substances contained in the PubChem Substance database, including descriptions of the conditions and the readouts (bioactivity levels) specific to the screening procedure.

Contains unique, validated chemical structures (small molecules) that can be searched using names, synonyms or keywords. The compound records may link to more than one PubChem Substance record if different depositors supplied the same structure. These Compound records reflect validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups. Additionally, calculated properties and descriptors are available for searching and filtering of chemical structures.

PubChem Substance records contain substance information electronically submitted to PubChem by depositors. This includes any chemical structure information submitted, as well as chemical names, comments, and links to the depositor's web site.

A database of citations and abstracts for biomedical literature from MEDLINE and additional life science journals. Links are provided when full text versions of the articles are available via PubMed Central (described below) or other websites.

A digital archive of full-text biomedical and life sciences journal literature, including clinical medicine and public health.

RefSeqGene A collection of human gene-specific reference genomic sequences. RefSeq gene is a subset of NCBI’s RefSeq database, and are defined based on review from curators of locus-specific databases and the genetic testing community. They form a stable foundation for reporting mutations, for establishing consistent intron and exon numbering conventions, and for defining the coordinates of other biologically significant variation. RefSeqGene is a part of the Locus Reference Genomic (LRG) Collaboration. Reference Sequence (RefSeq)

A collection of curated, non-redundant genomic DNA, transcript (RNA), and protein sequences produced by NCBI. RefSeqs provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. The RefSeq collection is accessed through the Nucleotide and Protein databases.

A collection of resources specifically designed to support the research of retroviruses, including a genotyping tool that uses the BLAST algorithm to identify the genotype of a query sequence an alignment tool for global alignment of multiple sequences an HIV-1 automatic sequence annotation tool and annotated maps of numerous retroviruses viewable in GenBank, FASTA, and graphic formats, with links to associated sequence records.

A summary of data for the SARS coronavirus (CoV), including links to the most recent sequence data and publications, links to other SARS related resources, and a pre-computed alignment of genome sequences from various isolates.

The Sequence Read Archive (SRA) stores sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Life Technologies AB SOLiD System®, Helicos Biosciences Heliscope®, Complete Genomics®, and Pacific Biosciences SMRT®.

Contains macromolecular 3D structures derived from the Protein Data Bank, as well as tools for their visualization and comparative analysis.

Contains the names and phylogenetic lineages of more than 160,000 organisms that have molecular data in the NCBI databases. New taxa are added to the Taxonomy database as data are deposited for them.

A database that contains sequences built from the existing primary sequence data in GenBank. The sequences and corresponding annotations are experimentally supported and have been published in a peer-reviewed scientific journal. TPA records are retrieved through the Nucleotide Database.

A repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects.

A wide range of resources, including a brief summary of the biology of viruses, links to viral genome sequences in Entrez Genome, and information about viral Reference Sequences, a collection of reference sequences for thousands of viral genomes.

An extension of the Influenza Virus Resource to other organisms, providing an interface to download sequence sets of selected viruses, analysis tools, including virus-specific BLAST pages, and genome annotation pipelines.

Downloads

BLAST executables for local use are provided for Solaris, LINUX, Windows, and MacOSX systems. See the README file in the ftp directory for more information. Pre-formatted databases for BLAST nucleotide, protein, and translated searches also are available for downloading under the db subdirectory.

Sequence databases for use with the stand-alone BLAST programs. The files in this directory are pre-formatted databases that are ready to use with BLAST.

This site provides full data records for CDD, along with individual Position Specific Scoring Matrices (PSSMs), mFASTA sequences and annotation data for each conserved domain. See the README file for full details.

This site provides full data extractions in XML and summary data in VCF format. It contains files with information about standard terms used in ClinVar, MedGen, and GTR.

Sequence databases in FASTA format for use with the stand-alone BLAST programs. These databases must be formatted using formatdb before they can be used with BLAST.

This site contains files for all sequence records in GenBank in the default flat file format. The files are organized by GenBank division, and the full contents are described in the README.genbank file.

The protein sequences corresponding to the translations of coding sequences (CDS) in GenBank are collected for each GenBank release..Please see the README file in the directory for more information.

This site contains three directories: DATA, GeneRIF and tools. The DATA directory contains files listing all data linked to GeneIDs along with subdirectories containing ASN.1 data for the Gene records. The GeneRIF (Gene References into Function) directory contains PubMed identifiers for articles describing the function of a single gene or interactions between products of two genes. Sample programs for manipulating gene data are provided in the tools directory. Please see the README file for details.

This site contains GEO data in two formats: SOFT (Simple Omnibus in Text Format) and MINiML (MIAME Notation in Markup Language). Summary text files and supplementary data are also available. Please see the README.TXT file for more information.

This site contains genome sequence and mapping data for organisms in Entrez Genome. The data are organized in directories for single species or groups of species. Mapping data are collected in the directory MapView and are organized by species. See the README file in the root directory and the README files in the species subdirectories for detailed information.

Contains directories for each genome that include available mapping data for current and previous builds of that genome.

This site contains the full taxonomy database along with files associating nucleotide and protein sequence records with their taxonomy IDs. See the taxdump_readme.txt and gi_taxid.readme files for more information.

This site provides data from the PubChem Substance, Compound and Bioassay databases for download via ftp. Full downloads of the databases are available along with daily, weekly and monthly updates for Substance and Compound. Substance and Compound data are provided in ASN.1, SDF and XML formats. See the README files for more information.

This site contains all nucleotide and protein sequence records in the Reference Sequence (RefSeq) collection. The ""release"" directory contains the most current release of the complete collection, while data for selected organisms (such as human, mouse and rat) are available in separate directories. Data are available in FASTA and flat file formats. See the README file for details.

This site contains SKY-CGH data in ASN.1, XML and EasySKYCGH formats. See the skycghreadme.txt file for more information.

Downloadable data for SNP.

This site contains next-generation sequencing data organized by the submitted sequencing project.

FTP download site for NCBI databases, tools, and utilities.

This site contains ASN.1 data for all records in MMDB along with VAST alignment data and the non-redundant PDB (nr-PDB) data sets. See the README file for more information.

This site contains the trace chromatogram data organized by species. Data include chromatogram, quality scores, FASTA sequences from automatic base calls, and other ancillary information in tab-delimited text as well as XML formats. See the README file for details.

This site contains the UniVec and UniVec_Core databases in FASTA format. See the README.uv file for details.

This site contains whole genome shotgun sequence data organized by the 4-digit project code. Data include GenBank and GenPept flat files, quality scores and summary statistics. See the README.genbank.wgs file for more information.

Open-access data generally include summaries of genotype/phenotype association studies, descriptions of the measured variables, and study documents, such as the protocol and questionnaires. Access to individual-level data, including phenotypic data tables and genotypes, requires varying levels of authorization.

NLM leases MEDLINE/PubMed to U.S. individuals or organizations.

Specifications for NCBI data in ASN.1 or DTD format are available on the Index of data_specs page. The "NCBI_data_conversion.html" links to the conversion tool.

A suite of tag sets for authoring and archiving journal articles as well as transferring journal articles from publishers to archives and between archives. There are four tag sets: Archiving and Interchange Tag Set - Created to enable an archive to capture as many of the structural and semantic components of existing printed and tagged journal material as conveniently as possible Journal Publishing Tag Set - Optimized for archives that wish to regularize and control their content, not to accept the sequence and arrangement presented to them by any particular publisher Article Authoring Tag Set - Designed for authoring new journal articles NCBI Book Tag Set - Written specifically to describe volumes for the NCBI online libraries.

This service allows users to download compound or substance records corresponding to a set of PubChem identifiers, which can be supplied manually or through a text file. Numerous download formats are available, including SDF, XML and SMILES.

The PMC Open-Access Subset is a relatively small part of the total collection of articles in PMC. Whereas the majority of articles in PMC are subject to traditional copyright restrictions, these articles are protected by copyright, but are made available under a Creative Commons or similar license that generally allows more liberal redistribution and reuse than a traditional copyright. Please refer to the license statement in each article for specific terms of use.

Subscribe to Web/RSS feeds for updates about NCBI resources.

Submissions

An online form that provides an interface for researchers, consortia and organizations to register their BioProjects. This serves as the starting point for the submission of genomic and genetic data for the study. The data does not need to be submitted at the time of BioProject registration.

Guidelines and instructions for submitting assertions about the pathogenicity of human genetic variants. These submissions can include summary data about a variant (variant level/aggregate data) support for variants per case (case-level) is in development.

Guidelines and requirements for submitting genotype and phenotype association data to dbGaP.

A web-based sequence submission tool for one or a few submissions to the GenBank database, designed to make the submission process quick and easy.

Tool for submission to the GenBank database of Barcode short nucleotide sequences from a standard genetic locus for use in species identification.

A stand-alone software tool developed by the NCBI for submitting and updating entries to public sequence databases (GenBank, EMBL, or DDBJ). It is capable of handling simple submissions that contain a single short mRNA sequence, complex submissions containing long sequences, multiple annotations, segmented sets of DNA, as well as sequences from phylogenetic and population studies with alignments. For simple submission, use the online submission tool BankIt instead.

A command-line program that automates the creation of sequence records for submission to GenBank using many of the same functions as Sequin. It is used primarily for submission of complete genomes and large batches of sequences.

Submit expression data, such as microarray, SAGE or mass spectrometry datasets to the NCBI Gene Expression Omnibus (GEO) database.

GeneRIF provides a simple mechanism to allow scientists to add to the functional annotation of genes in the Gene database.

Guidelines and instructions for registering laboratories and submitting genetic test information including clinical and research tests for germline or somatic test targets. GTR welcomes registration of cytogenetic, biochemical, and molecular tests for Mendelian disorders, pharmacogenetic phenotypes and complex panels.

The NIH Manuscript Submission (NIHMS) System is used to submit manuscripts that arise from NIH funding to the PubMed Central digital archive, in accordance with the NIH Public Access Policy and the law it implements. The law and Public Access Policy are intended to ensure that the public has access to the published results of NIH-funded research.

This site enables users to submit data to the PubChem Substance and BioAssay databases, including chemical structures, experimental biological activity results, annotations, siRNA data and more. It can also be used to update previously submitted records.

The SNP database tools page provides links to the general submission guidelines and to the submission handle request. The page has also two specific links for single- or batch submissions of the human variation data using Human Genome Variation Society nomenclature.

This link describes how submitters of SRA data can obtain a secure NCBI FTP site for their data, and also describes the allowed data formats and directory structures.

A single entry point for submitters to link to and find information about all of the data submission processes at NCBI. Currently, this serves as an interface for the registration of BioProjects and BioSamples and submission of data for WGS and GTR. Future additions to this site are planned.

This link describes how submitters of trace data can obtain a secure NCBI FTP site for their data, and also describes the allowed data formats and directory structures.

Tools

An interactive graphical viewer that allows users to explore variant calls, genotype calls and supporting evidence (such as aligned sequence reads) that have been produced by the 1000 Genomes Project.

This tool allows users to explore the characteristics of amino acids by comparing their structural and chemical properties, predicting protein sequence changes caused by mutations, viewing common substitutions, and browsing the functions of given residues in conserved domains.

Performs a BLAST search for similar sequences from selected complete eukaryotic and prokaryotic genomes.

Performs a BLAST search of the genomic sequences in the RefSeqGene/LRG set. The default display provides ready navigation to review alignments in the Graphics display.

This page links to a number of BLAST-related tutorials and guides, including a selection guide for BLAST algorithms, descriptions of BLAST output formats, explanations of the parameters for stand-alone BLAST, directions for setting up stand-alone BLAST on local machines and using the BLAST URL API.

Finds regions of local similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as to help identify members of gene families.

Allows you to retrieve records from many Entrez databases by uploading a file of GI or accession numbers from the Nucleotide or Protein databases, or a file of unique identifiers from other Entrez databases. Search results can be saved in various formats directly to a local file on your computer.

A stand-alone application for classifying protein sequences and investigating their evolutionary relationships. CDTree can import, analyze and update existing Conserved Domain (CDD) records and hierarchies, and also allows users to create their own. CDTree is tightly integrated with Entrez CDD and Cn3D, and allows users to create and update protein domain alignments.

COBALT is a protein multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST.

A stand-alone application for viewing 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, Macintosh, and UNIX and can be configured to receive data from most popular web browsers. Cn3D simultaneously displays structure, sequence, and alignment, and has powerful annotation and alignment editing features.

Part of the NCBI Bookshelf, Coffee Break combines reports on recent biomedical discoveries with use of NCBI tools. Each report incorporates interactive tutorials that show how NCBI bioinformatics tools are used as a part of the research process.

Displays the functional domains that make up a given protein sequence. It lists proteins with similar domain architectures and can retrieve proteins that contain particular combinations of domains.

Identifies the conserved domains present in a protein sequence. CD-Search uses RPS-BLAST (Reverse Position-Specific BLAST) to compare a query sequence against position-specific score matrices that have been prepared from conserved domain alignments present in the Conserved Domain Database (CDD).

Tools that provide access to data within NCBI's Entrez system outside of the regular web query interface. They provide a method of automating Entrez tasks within software applications. Each utility performs a specialized retrieval task, and can be used simply by writing a specially formatted URL.

A tool that allows users to construct an E-utility analysis pipeline using an online form, and then generates a Perl script to execute the pipeline.

Tool for aligning a query sequence (nucleotide or protein) to GenBank sequences included on microarray or SAGE platforms in the GEO database.

Displays the genetic codes for organisms in the Taxonomy database in tables and on a taxonomic tree.

This tool compares nucleotide or protein sequences to genomic sequence databases and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST) algorithm.

A genome browser for interactive navigation of eukaryotic RefSeq genome assemblies with comprehensive inspection of gene, expression, variation and other annotations. GDV offers easy-to-load analytical track pre-configurations, a menu of data tracks for easy display and customization, and supports upload and analysis of user data. This browser also enables the production of displays for publishing.

An online tool that assists in the production of journal quality figures of annotations on an ideogram or sequence representation of an assembly.

NCBI's Remap tool allows users to project annotation data and convert locations of features from one genomic assembly to another or to RefSeqGene sequences through a base by base analysis. Options are provided to adjust the stringency of remapping, and summary results are displayed on the web page. Full results can be downloaded for viewing in NCBI's Genome Workbench graphical viewer, and annotation data for the remapped features, as well as summary data, is also available for download.

An integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix these data with your own data.

A service that allows third parties to link directly from PubMed and other Entrez database records to relevant web-accessible resources beyond the Entrez system. Examples of LinkOut resources include full-text publications, biological databases, consumer health information and research tools.

Provides special browsing capabilities of maps and assembled sequences for a subset of organisms. You can view and search an organism's complete genome, display maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest.

An interactive web application that enables users to visualize multiple alignments created by database search results or other software applications. The MSA Viewer allows users to upload an alignment and set a master sequence, and to explore the data using features such as zooming and changing of coloration.

Provides information on new and updated resources and NCBI research and development projects. The News site contains feature articles highlighting services, resource features and tools, as well as frequent postings describing important announcements regarding key datasets and services of interest to the user community. Links to NCBI's social media sites along and a list of available RSS feeds and Email listservs are provided.

A set of software and data exchange specifications used by NCBI to produce portable, modular software for molecular biology. The software in the Toolbox is primarily designed to read records in Abstract Syntax Notation 1 (ASN.1) format, an International Standards Organization (ISO) data representation format.

A public domain quality assurance software package that facilitates the assessment of multiplex short tandem repeat (STR) DNA profiles based on laboratory-specific protocols. OSIRIS evaluates the raw electrophoresis data using an independently derived mathematically-based sizing algorithm. It offers two new peak quality measures - fit level and sizing residual. It can be customized to accommodate laboratory-specific signatures such as background noise settings, customized naming conventions and additional internal laboratory controls.

A graphical analysis tool that finds all open reading frames in a user's sequence or in a sequence already in the database. Sixteen different genetic codes can be used. The deduced amino acid sequence can be saved in various formats and searched against protein databases using BLAST.

Allows users to display, sort, subset and download position-specific score matrices (PSSMs) either from CDD records or from Position Specific Iterated (PSI)-BLAST protein searches. The tool also can align a query protein to the PSSM and highlight positions of high conservation.

Supports finding human phenotype/genotype relationships with queries by phenotype, chromosome location, gene, and SNP identifiers. Currently includes information from dbGaP, the NHGRI GWAS Catalog, and GTeX. Displays results on the genome, on sequence, or in tables for download.

The Primer-BLAST tool uses Primer3 to design PCR primers to a sequence template. The potential products are then automatically analyzed with a BLAST search against user specified databases, to check the specificity to the target intended.

A utility for computing alignment of proteins to genomic nucleotide sequence. It is based on a variation of the Needleman Wunsch global alignment algorithm and specifically accounts for introns and splice signals. Due to this algorithm, ProSplign is accurate in determining splice sites and tolerant to sequencing errors.

PUG provides access to PubChem services via a programmatic interface. PUG allows users to download data, initiate chemical structure searches, standardize chemical structures and interact with the E-utilities. PUG can be accessed using either standard URLs or via SOAP.

Standardization, in PubChem terminology, is the processing of chemical structures in the same way used to create PubChem Compound records from contributors' original structures. This service lets users see how PubChem would handle any structure they would like to submit.

PubChem Structure Search allows the PubChem Compound Database to be queried by chemical structure or chemical structure pattern. The PubChem Sketcher allows a query to be drawn manually. Users may also specify the structural query input by PubChem Compound Identifier (CID), SMILES, SMARTS, InChI, Molecular Formula, or by upload of a supported structure file format.

A specialized PubMed search form targeted to clinicians and health services researchers. The page simplifies searching by clinical study category, finding systematic reviews and searching the medical genetics literature.

A collection of web and flash tutorials on PubMed searching and linking, saving searches in MyNCBI, using MeSH and other PubMed services.

The Related Structures tool allows users to find 3D structures from the Molecular Modeling Database (MMDB) that are similar in sequence to a query protein. Although the query protein may not yet have a resolved structure, the 3D shape of a similar protein sequence can shed light on the putative shape and biological function of the query protein.

A variety of tools are available for searching the SNP database, allowing search by genotype, method, population, submitter, markers and sequence similarity using BLAST. These are linked under ""Search"" on the left side bar of the dbSNP main page.

Sequence Cytogenetic Conversion Service An online tool that converts sequence and cytogenetic coordinates for human, rat, mouse and fruit fly genomic assemblies. Sequence Viewer

Provides a configurable graphical display of a nucleotide or protein sequence and features that have been annotated on that sequence. In addition to use on NCBI sequence database pages, this viewer is available as an embeddable webpage component. Detailed documentation including an API Reference guide is available for developers wishing to embed the viewer in their own pages.

A utility for computing cDNA-to-Genomic sequence alignments. It is based on a variation of the Needleman-Wunsch global alignment algorithm and specifically accounts for introns and splice signals. Due to this algorithm, Splign is accurate in determining splice sites and tolerant to sequencing errors.

Supports searching the taxonomy tree using partial taxonomic names, common names, wild cards and phonetically similar names. For each taxonomic node, the tool provides links to all data in Entrez for that node, displays the lineage, and provides links to external sites related to the node.

Generates a taxonomic tree for a selected group of organisms. Users can upload a file of taxonomy IDs or names, or they can enter names or IDs directly.

Displays the number of taxonomic nodes in the database for a given rank and date of inclusion.

Displays the current status of a set of taxonomic nodes or IDs.

A tool for creating and displaying phylogenetic tree data. Tree Viewer enables analysis of your own sequence data, produces printable vector images as PDFs, and can be embedded in a webpage.

Variation Viewer A genomic browser to search and view genomic variations listed in dbSNP, dbVar, and ClinVar databases. Searches can be performed using chromosomal location, gene symbol, phenotype, or variant IDs from dbSNP and dbVar. The browser enables exploration of results in a dynamic graphical sequence viewer with annotated tables of variations. VecScreen

A system for quickly identifying segments of a nucleic acid sequence that may be of vector origin. VecScreen searches a query sequence for segments that match any sequence in a specialized non-redundant vector database (UniVec).

A computer algorithm that identifies similar protein 3-dimensional structures. Structure neighbors for every structure in MMDB are pre-computed and accessible via links on the MMDB Structure Summary pages. These neighbors can be used to identify distant homologs that cannot be recognized by sequence comparison alone.

This tool helps identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus.


The Plant List &mdash A working list for all plant species

Enter a Genus (eg Ocimum) or genus and species (eg Ocimum basilicum).

? will match a single character. * will match any number of characters. Use at least three letters in the genus name if you include a ? or * .

The Plant List (TPL) was a working list of all known plant species produced by the botanical community in response to Target 1 of the 2002-2010 Global Strategy for Plant Conservation (GSPC). TPL has been static since 2013, but was used as the starting point for the Taxonomic Backbone of the World Flora Online (WFO) , and updated information can be found at www.worldfloraonline.org.

WFO is being developed by a consortium of leading botanical institutions worldwide in response to the 2011-2020 GSPC’s updated Target 1: to achieve an online Flora of all known plants by 2020. WFO welcomes feedback from users for improvements to its Taxonomic Backbone which is curated by a growing community of WFO Taxonomic Expert Networks (TENs).

The Plant List is a working list of all known plant species. It aims to be comprehensive for species of Vascular plant (flowering plants, conifers, ferns and their allies) and of Bryophytes (mosses and liverworts).

Collaboration between the Royal Botanic Gardens, Kew and Missouri Botanical Garden enabled the creation of The Plant List by combining multiple checklist data sets held by these institutions and other collaborators.

Version 1.1 (September 2013) replaces Version 1.0 which remains accessible here. Version 1.1 includes new data sets, updated versions of the original data sets and improved algorithms to resolve logical conflicts between those data sets. The differences between versions are summarised here.

The Plant List provides the Accepted Latin name for most species, with links to all Synonyms by which that species has been known. Around 20% of names are unresolved indicating that the data sources included provided no evidence or view as to whether the name should be treated as accepted or not, or there were conflicting opinions that could not be readily resolved.

The Plant List is not perfect and represents work in progress. Our aims remain to produce a ‘best effort’ list, to demonstrate progress and to stimulate further work. Important limitations are summarised here.

Summary Statistics

The Plant List includes 1,064,035 scientific plant names of species rank. Of these 350,699 are accepted species names.

The Plant List contains 642 plant families and 17,020 plant genera.

The status of the 1,064,035 species names, are as follows:

Status Total
Accepted 350,699 33.0%
Synonym 470,624 44.2%
Unresolved 242,712 22.8%

Browse

Click on the major plant group of interest to explore the taxonomic hierarchy embedded within The Plant List .

Work down the taxonomic hierarchy from Major Group (to find out which Families belong to each), to Family (to discover the Genera belonging to each) and finally Genus (to list the Species in each).


You can do this!

Plant Identification can have a steep learning curve but it gets easier the more you know. After you start to recognize what makes an oak an oak, or a maple a maple, then you only have to figure out which specific species it is you are halfway there! Then, you will find, many plants can be quickly identified by, single, easily observable traits. For example, the young ecologist above is checking the leafstalk on this maple leaf for a milky sap, a sure sign that it is a Norway Maple because no other maple has that milky sap. You will learn tips and tricks like this, from nurseries, other gardeners, or online, as you go about your search. For fun and practice try an online quiz or go for a hike or walk and collect some samples to spend some time at home with a field guide. Learning the names of plants is like being introduced to new friends and once you are familiar with them, and their “personalities” you can recognize them even in a crowd of other vegetation. And of course, feel free to email us at [email protected] with any plant ID questions.

Add a Plant ID to Your Map

Adding a Plant ID to your map starts with adding the plant object. First, choose the Third option in the Tool Shed. This will bring up a row of objects along the bottom of the map. Select the icon you like which best represents the plant you are adding. There are three options for trees, shrubs, or flowers and several more for other various types of plants. The image itself is for your personal design or organization.

After selecting the icon for your plant, simply click on the map where you would like to place it. A corner point of a box will appear with your plant icon. Move the mouse to drag open the box to the size you desire and click your mouse to place the opposite corner of the box.

Double click on the newly placed plant object. An info-window will pop-up where you can add details and characteristics. Select Basic Information from the left hand menu and give your plant a personal title, anything you like. You can then Set the Species using the common or scientific name in the lower menu. Just start typing and a drop down menu will give you possible selections. Choose the correct species and then Save your entry.


Watch the video: Παχύρα - Το Φυτό που Φέρνει Θετική Ενέργεια και Χρήματα στο Σπίτι. The Gardener (August 2022).