Nightingale: web components for protein feature visualization.

Motivation: The visualization of biological data is a fundamental technique that enables researchers to understand and explain biology. Some of these visualizations have become iconic, for instance: tree views for taxonomy, cartoon rendering of 3D protein structures or tracks to represent features in a gene or protein, for instance in a genome browser. Nightingale provides visualizations in the context of proteins and protein features. Results: Nightingale is a library of re-usable data visualization web components that are currently used by UniProt and InterPro, among other projects. The components can be used to display protein sequence features, variants, interaction data, 3D structure, etc. These components are flexible, allowing users to easily view multiple data sources within the same context, as well as compose these components to create a customized view. Availability and implementation: Nightingale examples and documentation are freely available at https://ebi-webcomponents.github.io/nightingale/. It is distributed under the MIT license, and its source code can be found at https://github.com/ebi-webcomponents/nightingale.

MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues.

An increasingly common output arising from the analysis of shotgun metagenomic datasets is the generation of metagenome-assembled genomes (MAGs), with tens of thousands of MAGs now described in the literature. However, the discovery and comparison of these MAG collections is hampered by the lack of uniformity in their generation, annotation and storage. To address this, we have developed MGnify Genomes, a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes. Genomes within a biome-specific catalogue are organised into species clusters. For species that contain multiple conspecific genomes, the highest quality genome is selected as the representative, always prioritising an isolate genome over a MAG. The species representative sequences and annotations can be visualised on the MGnify website and the full catalogue and associated analysis outputs can be downloaded from MGnify servers. A suite of online search tools is provided allowing users to compare their own sequences, ranging from a gene to sets of genomes, against the catalogues. Seven biomes are available currently, comprising over 300,000 genomes that represent 11,048 non-redundant species, and include 36 taxonomic classes not currently represented by cultured genomes. MGnify Genomes is available at https://www.ebi.ac.uk/metagenomics/browse/genomes/.

InterPro in 2022.

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (version 90.0) and its associated software, including updates to data content and to the website. These developments extend and enrich the information provided by InterPro, and provide a more user friendly access to the data. Additionally, we have worked on adding Pfam website features to the InterPro website, as the Pfam website will be retired in late 2022. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB. Moreover, we report the development of a card game as a method of engaging the non-scientific community. Finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction.

The InterPro protein families and domains database: 20 years on.

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing equivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification. Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation. Here, we report the status of InterPro (version 81.0) in its 20th year of operation, and its associated software, including updates to database content, the release of a new website and REST API, and performance improvements in InterProScan.

Pfam: The protein families database in 2021.

The Pfam database is a widely used resource for classifying protein sequences into families and domains. Since Pfam was last described in this journal, over 350 new families have been added in Pfam 33.1 and numerous improvements have been made to existing entries. To facilitate research on COVID-19, we have revised the Pfam entries that cover the SARS-CoV-2 proteome, and built new entries for regions that were not covered by Pfam. We have reintroduced Pfam-B which provides an automatically generated supplement to Pfam and contains 136 730 novel clusters of sequences that are not yet matched by a Pfam family. The new Pfam-B is based on a clustering by the MMseqs2 software. We have compared all of the regions in the RepeatsDB to those in Pfam and have started to use the results to build and refine Pfam repeat families. Pfam is freely available for browsing and download at http://pfam.xfam.org/.

Ecografía doppler de la arteria pulmonar como indicador de madurez pulmonar fetal, Cuenca ­ Ecuador / Doppler ultrasound of the pulmonary artery as fetal lung maturity indicator, Cuenca - Ecuador

Introducción: la flujometría de la arteria pulmonar en fetos sanos puede ser un estudio predictor de la madurez pulmonar, lo que conlleva a un impacto en la disminución de la mortalidad perinatal.Objetivo: establecer el índice de tiempo de aceleración/tiempo de eyección de la arteria pulmonar (TA/TE) como un indicador de madurez pulmonar fetal en gestantes entre 26 y 40 semanas de gestación (SG), usuarias del Hospital Especializado Fundación Humanitaria Pablo Jaramillo Crespo, periodo 2017.Métodos: estudio de validación de prueba diagnóstica. Se evaluó la flujometría de la arteria pulmonar por ecografía doppler en 300 fetos sanos de gestantes entre 15 y 45 años de edad. Para la recolección de datos se utilizó encuestas y para la determinación de la validez se usó los estadísticos sensibilidad (S), especificidad (E), valor predictivo positivo (VPP) y valor predictivo negativo (VPN). Resultados: el valor del índice TA/TE de la arteria pulmonar fue 0.216 para las gestantes entre 26-28 SG; de 0.253 entre 29-31 SG; de 0.279 entre 32-34 SG; de 0.315 para las gestantes entre 35-37 SG y de 0.349 entre 38-40 SG. Las 37 SG en punto de corte fue de 0.320; el área ROC fue 0.98 con una S: 95.2%, E: 97.2%. VPP 93.0% y VPN 98.1%.Conclusiones: el índice TA/TE de la arteria pulmonar demostró correlación con la edad gestacional. Un índice TA/TE de 0.320, como punto de corte, predice madurez pulmonar fetal (AU);

Introduction: pulmonary artery flow metric in healthy fetuses can be a predictive study of lung maturity, which leads to an impact on the decrease in perinatal mortality.Objective: to establish the ratio of pulmonary artery acceleration time to ejection time (AT/ET) as an indicator of fetal lung maturity in pregnant women from 26 to 40 weeks of gestation (WG), users of the "Hospital Especializado Fundación Humanitaria Pablo Jaramillo Crespo", period 2017.Methods: A validity study of diagnostic tests was carried out. Pulmonary artery flow metric was evaluated by Doppler ultrasound in 300 healthy fetuses of pregnant women between 15 to 45 years old. Surveys were used to collect data. Sensitivity (S), specificity (E), positive predictive value (PPV) and negative predictive value (NPV) were used to determine validity.Results: the value of the TA / TE index of the pulmonary artery was 0.216 for pregnant women between 26-28 WG; of 0.253 between 29-31 WG; 0.279 between 32-34 WG; 0.315 for pregnant women between 35-37 WG and 0.349 between 38-40 WG. The 37 WG at the cut-off point was 0.320; the ROC area was 0.98 with a S: 95.2%, E: 97.2%. The PPV 93.0% and NPV 98.1%.Conclusions: the AT/ET ratio of pulmonary artery showed correlation with gestational age. An AT/ET ratio of 0.320, as a cut-off point, predicts fetal lung maturity (AU);

Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.

Genome3D (https://www.genome3d.eu) is a freely available resource that provides consensus structural annotations for representative protein sequences taken from a selection of model organisms. Since the last NAR update in 2015, the method of data submission has been overhauled, with annotations now being 'pushed' to the database via an API. As a result, contributing groups are now able to manage their own structural annotations, making the resource more flexible and maintainable. The new submission protocol brings a number of additional benefits including: providing instant validation of data and avoiding the requirement to synchronise releases between resources. It also makes it possible to implement the submission of these structural annotations as an automated part of existing internal workflows. In turn, these improvements facilitate Genome3D being opened up to new prediction algorithms and groups. For the latest release of Genome3D (v2.1), the underlying dataset of sequences used as prediction targets has been updated using the latest reference proteomes available in UniProtKB. A number of new reference proteomes have also been added of particular interest to the wider scientific community: cow, pig, wheat and mycobacterium tuberculosis. These additions, along with improvements to the underlying predictions from contributing resources, has ensured that the number of annotations in Genome3D has nearly doubled since the last NAR update article. The new API has also been used to facilitate the dissemination of Genome3D data into InterPro, thereby widening the visibility of both the annotation data and annotation algorithms.

Intraepithelial cervical lesions in indigenous in Ecuador / Lesiones intraepiteliales cervicales en indígenas del Ecuador

The aim of this research was to determine the prevalence of cervical intraepithelial lesions in indigenous women of Ecuador 2017. A descriptive study was performed. Population was formed by 2489 indigenous women aged 15 to 64 years old, of which 396 users were chosen by spontaneous demand. Frequency values and percentages were taken from qualitative variables, while mean and standard deviation were taken from quantitative variables. Prevalence of intraepithelial lesions was 13,8%. Average age was 31 years old. Uncertain importance's squamous atypical cells were higher in 30-to-39-year-old group (46,7%). Non-specific atypical glandular cells were observed in 66,7% of 30-to-39-year-old group. Low-grade intraepithelial lesions were majorly found in 20-to-29-year-old group (43,8%). High-grade intraepithelial lesions were also seen in 20-to-29-year-old group. Conclusions were: prevalence of intraepithelial lesions in indigenous women of Ecuador was higher than 10% of reported in other studies, and more frequent in those aged 20 and 39 years old

El objetivo de esta investigación fue determinar la prevalencia de lesiones intraepiteliales cervicales en mujeres indígenas del Ecuador 2017. Se realizó un estudio descriptivo. La población estuvo compuesta por 2489 mujeres indígenas de 15 a 64 años, de las cuales 396 usuarias fueron elegidas por demanda espontánea. De las variables cualitativas se obtuvieron los valores de frecuencia y porcentajes, y de las cuantitativas la media y la desviación estándar. La prevalencia de las lesiones intraepiteliales fue del 13,8%. La edad promedio fue 31 años. Las células escamosas atípicas de importancia incierta fueron mayores en el grupo de edad de 30 a 39 años (46,7%). Se observaron células atípicas glandulares no específicas en el 66,7% en el grupo de 30 y 39 años de edad. Las lesiones intraepiteliales de bajo grado se presentaron más en el grupo de 20 y 29 años (43,8%). Las lesiones intraepiteliales de alto grado se identificaron también en el grupo de 20 a 29 años de edad. Las conclusiones fueron: la prevalencia de lesiones intraepiteliales en las mujeres indígenas del Ecuador fue superior al 10% de las reportadas en otros estudios, y más frecuente en aquellas de 20 y 39 años de edad

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website. These developments extend and enrich the information provided by InterPro, and provide greater flexibility in terms of data access. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB, and discuss how our evaluation of residue coverage may help guide future curation activities.

Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes.

Automatic annotation of protein function is routinely applied to newly sequenced genomes. While this provides a fine-grained view of an organism's functional protein repertoire, proteins, more commonly function in a coordinated manner, such as in pathways or multimeric complexes. Genome Properties (GPs) define such functional entities as a series of steps, originally described by either TIGRFAMs or Pfam entries. To increase the scope of coverage, we have migrated GPs to function as a companion resource utilizing InterPro entries. Having introduced GPs-specific versioned releases, we provide software and data via a GitHub repository, and have developed a new web interface to GPs (available at https://www.ebi.ac.uk/interpro/genomeproperties). In addition to exploring each of the 1286 GPs, the website contains GPs pre-calculated for a representative set of proteomes; these results can be used to profile GPs phylogenetically via an interactive viewer. Users can upload novel data to the viewer for comparison with the pre-calculated results. Over the last year, we have added ∼700 new GPs, increasing the coverage of eukaryotic systems, as well as increasing general coverage through automatic generation of GPs from related resources. All data are freely available via the website and the GitHub repository.

The Pfam protein families database in 2019.

The last few years have witnessed significant changes in Pfam (https://pfam.xfam.org). The number of families has grown substantially to a total of 17,929 in release 32.0. New additions have been coupled with efforts to improve existing families, including refinement of domain boundaries, their classification into Pfam clans, as well as their functional annotation. We recently began to collaborate with the RepeatsDB resource to improve the definition of tandem repeat families within Pfam. We carried out a significant comparison to the structural classification database, namely the Evolutionary Classification of Protein Domains (ECOD) that led to the creation of 825 new families based on their set of uncharacterized families (EUFs). Furthermore, we also connected Pfam entries to the Sequence Ontology (SO) through mapping of the Pfam type definitions to SO terms. Since Pfam has many community contributors, we recently enabled the linking between authorship of all Pfam entries with the corresponding authors' ORCID identifiers. This effectively permits authors to claim credit for their Pfam curation and link them to their ORCID record.

Validación de la Escala de Desesperanza de Beck en pacientes con riesgo suicida / Validation of the Beck Hopelessness Scale in patients with suicide risk

Introducción. Pocas escalas se han validado en castellano para el riesgo suicida y en ninguna de ellas se ha hallado la validez predictiva. Objetivo. Determinar la validez y confiabilidad de la Escala de Desesperanza de Beck en pacientes con suicidabilidad que acuden a consulta especializada. Métodos. Se aplicaron la Escala de Desesperanza de Beck, el Inventario de Razones para Vivir y el Cuestionario de Comportamiento Suicida a pacientes con suicidabilidad que asistieron a consulta externa y urgencias. A los 30 días se realizó una valoración para determinar la validez predictiva del intento suicida o suicidio. Resultados. Se evaluaron 244 pacientes con una edad promedio de 30,7 años±13,2; la mayoría de ellos fueron mujeres. La consistencia interna de la Escala de Desesperanza de Beck es de 0,9 (fórmula 20 de Kuder-Richardson). Se encontraron 4 dimensiones que explican el 50% de la varianza. Tuvo una correlación positiva con el Cuestionario de Comportamiento Suicida (Spearman 0,48, p<0,001), número de intentos suicidas (Spearman 0,25, p<0,001), y severidad del riesgo suicida (Spearman 0,23, p<0,001). La correlación con el Inventario de Razones para Vivir fue negativa (Spearman -0,52, p<0,001). Con un punto de corte ≥12 el valor predictivo negativo fue de 98,4% (IC 95%: 94,2-99,8), y el valor predictivo positivo fue de 14,8% (IC 95%: 6,6-27,1). Conclusión. La Escala de Desesperanza de Beck en pacientes colombianos con suicidabilidad presenta unas dimensiones similares a la versión original, con adecuada confiabilidad y moderada validez, tanto concurrente como predictiva

Introduction. Only a few scales have been validated in Spanish for the assessment of suicide risk, and none of them have achieved predictive validity. Objective. To determine the validity and reliability of the Beck Hopelessness Scale in patients with suicide risk attending the specialist clinic. Methods. The Beck Hopelessness Scale, reasons for living inventory, and the suicide behaviour questionnaire were applied in patients with suicide risk attending the psychiatric clinic and the emergency department. A new assessment was made 30 days later to determine the predictive validity of suicide or suicide attempt. Results. The evaluation included a total of 244 patients, with a mean age of 30.7±13.2 years, and the majority were women. The internal consistency was .9 (Kuder-Richardson formula 20). Four dimensions were found which accounted for 50% of the variance. It was positively correlated with the suicidal behaviour questionnaire (Spearman .48, P<.001), number of suicide attempts (Spearman .25, P<.001), severity of suicide risk (Spearman .23, P<.001). The correlation with the reasons for living inventory was negative (Spearman -52, P<.001). With a cut-off ≥12, the negative predictive value was 98.4% (95% CI: 94.2-99.8), and the positive predictive value was 14.8% (95% CI: 6.6-27.1). Conclusion. The Beck Hopelessness Scale in Colombian patients with suicidality shows results similar to the original version, with adequate reliability and moderate concurrent and predictive validity

Validation of the Beck Hopelessness Scale in patients with suicide risk. / Validación de la Escala de Desesperanza de Beck en pacientes con riesgo suicida.

INTRODUCTION: Only a few scales have been validated in Spanish for the assessment of suicide risk, and none of them have achieved predictive validity. OBJECTIVE: To determine the validity and reliability of the Beck Hopelessness Scale in patients with suicide risk attending the specialist clinic. METHODS: The Beck Hopelessness Scale, reasons for living inventory, and the suicide behaviour questionnaire were applied in patients with suicide risk attending the psychiatric clinic and the emergency department. A new assessment was made 30 days later to determine the predictive validity of suicide or suicide attempt. RESULTS: The evaluation included a total of 244 patients, with a mean age of 30.7±13.2 years, and the majority were women. The internal consistency was .9 (Kuder-Richardson formula 20). Four dimensions were found which accounted for 50% of the variance. It was positively correlated with the suicidal behaviour questionnaire (Spearman .48, P<.001), number of suicide attempts (Spearman .25, P<.001), severity of suicide risk (Spearman .23, P<.001). The correlation with the reasons for living inventory was negative (Spearman -.52, P<.001). With a cut-off ≥12, the negative predictive value was 98.4% (95% CI: 94.2-99.8), and the positive predictive value was 14.8% (95% CI: 6.6-27.1). CONCLUSION: The Beck Hopelessness Scale in Colombian patients with suicidality shows results similar to the original version, with adequate reliability and moderate concurrent and predictive validity.

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies.

EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons.

Platelet proteome reveals novel pathways of platelet activation and platelet-mediated immunoregulation in dengue.

Dengue is the most prevalent human arbovirus disease worldwide. Dengue virus (DENV) infection causes syndromes varying from self-limiting febrile illness to severe dengue. Although dengue pathophysiology is not completely understood, it is widely accepted that increased inflammation plays important roles in dengue pathogenesis. Platelets are blood cells classically known as effectors of hemostasis which have been increasingly recognized to have major immune and inflammatory activities. Nevertheless, the phenotype and effector functions of platelets in dengue pathogenesis are not completely understood. Here we used quantitative proteomics to investigate the protein content of platelets in clinical samples from patients with dengue compared to platelets from healthy donors. Our assays revealed a set of 252 differentially abundant proteins. In silico analyses associated these proteins with key molecular events including platelet activation and inflammatory responses, and with events not previously attributed to platelets during dengue infection including antigen processing and presentation, proteasome activity, and expression of histones. From these results, we conducted functional assays using samples from a larger cohort of patients and demonstrated evidence for platelet activation indicated by P-selectin (CD62P) translocation and secretion of granule-stored chemokines by platelets. In addition, we found evidence that DENV infection triggers HLA class I synthesis and surface expression by a mechanism depending on functional proteasome activity. Furthermore, we demonstrate that cell-free histone H2A released during dengue infection binds to platelets, increasing platelet activation. These findings are consistent with functional importance of HLA class I, proteasome subunits, and histones that we found exclusively in proteome analysis of platelets in samples from dengue patients. Our study provides the first in-depth characterization of the platelet proteome in dengue, and sheds light on new mechanisms of platelet activation and platelet-mediated immune and inflammatory responses.

The Pfam protein families database: towards a more sustainable future.

In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automatically-generated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool.

Formation of a fluorous/organic biphasic supramolecular octopus assembly for enhanced porphyrin phosphorescence in air.

The trinuclear triangle-shaped system [tris{3,5-bis(heptafluoropropyl)-1,2,4-triazolatosilver(I)}] (1) and the multi-armed square-shaped metalloporphyrin PtOEP or the free porphyrin base H2OEP serve as excellent octopus hosts (OEP=2,3,7,8,12,13,17,18-octaethyl-21H,23H-porphine). Coupling of the fluorous/organic molecular octopi 1 and H2OEP or PtOEP by strong quadrupole-quadrupole and metal-π interactions affords the supramolecular assemblies [1⋅PtOEP] or [1⋅H2OEP] (2 a), which feature nanoscopic cavities surrounding the upper triangular and lower square cores. The fluorous/organic biphasic configuration of [1⋅PtOEP] leads to an increase in the phosphorescence of PtOEP under ambient conditions. Guest molecules can be included in the biphasic double-octopus assembly in three different site-selective modes.

PPI layouts: BioJS components for the display of Protein-Protein Interactions.

SUMMARY: We present two web-based components for the display of Protein-Protein Interaction networks using different self-organizing layout methods: force-directed and circular. These components conform to the BioJS standard and can be rendered in an HTML5-compliant browser without the need for third-party plugins. We provide examples of interaction networks and how the components can be used to visualize them, and refer to a more complex tool that uses these components. AVAILABILITY: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7753.

BioJS: an open source standard for biological visualisation - its status in 2014.

BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi.ac.uk/tools/biojs/. The source code for all components is available for ready use at https://github.com/biojs/biojs.

A web-based protein interaction network visualizer.

BACKGROUND: Interaction between proteins is one of the most important mechanisms in the execution of cellular functions. The study of these interactions has provided insight into the functioning of an organism's processes. As of October 2013, Homo sapiens had over 170000 Protein-Protein interactions (PPI) registered in the Interologous Interaction Database, which is only one of the many public resources where protein interactions can be accessed. These numbers exemplify the volume of data that research on the topic has generated. Visualization of large data sets is a well known strategy to make sense of information, and protein interaction data is no exception. There are several tools that allow the exploration of this data, providing different methods to visualize protein network interactions. However, there is still no native web tool that allows this data to be explored interactively online. RESULTS: Given the advances that web technologies have made recently it is time to bring these interactive views to the web to provide an easily accessible forum to visualize PPI. We have created a Web-based Protein Interaction Network Visualizer: PINV, an open source, native web application that facilitates the visualization of protein interactions (http://biosual.cbio.uct.ac.za/pinv.html). We developed PINV as a set of components that follow the protocol defined in BioJS and use the D3 library to create the graphic layouts. We demonstrate the use of PINV with multi-organism interaction networks for a predicted target from Mycobacterium tuberculosis, its interacting partners and its orthologs. CONCLUSIONS: The resultant tool provides an attractive view of complex, fully interactive networks with components that allow the querying, filtering and manipulation of the visible subset. Moreover, as a web resource, PINV simplifies sharing and publishing, activities which are vital in today's research collaborative environments. The source code is freely available for download at https://github.com/4ndr01d3/biosual.